Phosphorus in PDB 1akh: Mat A1/ALPHA2/Dna Ternary Complex

Protein crystallography data

The structure of Mat A1/ALPHA2/Dna Ternary Complex, PDB code: 1akh was solved by T.Li, Y.Jin, A.K.Vershon, C.Wolberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.50
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 132.250, 132.250, 45.250, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 30.2

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Phosphorus atom in the Mat A1/ALPHA2/Dna Ternary Complex (pdb code 1akh). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 40 binding sites of Phosphorus where determined in the Mat A1/ALPHA2/Dna Ternary Complex, PDB code: 1akh:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 40 in 1akh

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Phosphorus binding site 1 out of 40 in the Mat A1/ALPHA2/Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Mat A1/ALPHA2/Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P2

b:55.7
occ:1.00
 P C:DA2 0.0 55.7 1.0
OP1 C:DA2 1.5 51.5 1.0
OP2 C:DA2 1.5 54.0 1.0
O5' C:DA2 1.6 47.3 1.0
O3' C:DT1 1.6 45.6 1.0
C5' C:DA2 2.6 39.2 1.0
C3' C:DT1 2.6 36.8 1.0
C2' C:DT1 3.5 30.8 1.0
C4' C:DA2 3.8 38.9 1.0
C4' C:DT1 3.9 29.9 1.0
O4' C:DA2 4.0 31.8 1.0
C8 C:DA2 4.2 22.8 1.0
C3' C:DA2 4.4 39.3 1.0
C5' C:DT1 4.6 35.8 1.0
C2' C:DA2 4.7 38.7 1.0
C1' C:DT1 4.8 25.2 1.0
C1' C:DA2 4.9 29.9 1.0
O4' C:DT1 4.9 20.2 1.0
N9 C:DA2 5.0 27.6 1.0

Phosphorus binding site 2 out of 40 in 1akh

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Phosphorus binding site 2 out of 40 in the Mat A1/ALPHA2/Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Mat A1/ALPHA2/Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P3

b:45.9
occ:1.00
 P C:DC3 0.0 45.9 1.0
OP2 C:DC3 1.5 50.3 1.0
OP1 C:DC3 1.5 50.4 1.0
O5' C:DC3 1.6 35.1 1.0
O3' C:DA2 1.6 45.0 1.0
C5' C:DC3 2.6 31.5 1.0
C3' C:DA2 2.6 39.3 1.0
NZ B:LYS177 3.2 40.4 1.0
C2' C:DA2 3.2 38.7 1.0
O C:HOH600 3.5 36.7 1.0
O B:HOH601 3.6 37.1 1.0
NH2 B:ARG184 3.9 23.0 1.0
C4' C:DC3 3.9 30.1 1.0
C4' C:DA2 3.9 38.9 1.0
CE B:LYS177 4.2 48.6 1.0
C3' C:DC3 4.3 29.3 1.0
C1' C:DA2 4.3 29.9 1.0
O4' C:DC3 4.5 29.6 1.0
CZ B:ARG184 4.6 20.4 1.0
NH1 B:ARG184 4.6 13.9 1.0
C6 C:DC3 4.7 17.9 1.0
O4' C:DA2 4.7 31.8 1.0
CD2 B:TYR156 4.8 15.2 1.0

Phosphorus binding site 3 out of 40 in 1akh

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Phosphorus binding site 3 out of 40 in the Mat A1/ALPHA2/Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Mat A1/ALPHA2/Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P4

b:34.7
occ:1.00
 P C:DA4 0.0 34.7 1.0
OP1 C:DA4 1.5 33.9 1.0
OP2 C:DA4 1.5 28.0 1.0
O5' C:DA4 1.6 28.0 1.0
O3' C:DC3 1.6 25.3 1.0
C3' C:DC3 2.6 29.3 1.0
C5' C:DA4 2.6 27.0 1.0
C2' C:DC3 3.1 35.7 1.0
NE B:ARG184 3.7 13.3 1.0
CE2 B:TYR156 3.9 10.2 1.0
C4' C:DA4 3.9 25.7 1.0
C4' C:DC3 3.9 30.1 1.0
NH2 B:ARG184 3.9 23.0 1.0
C8 C:DA4 4.1 19.3 1.0
O C:HOH617 4.1 3.2 0.5
OH B:TYR156 4.1 26.5 1.0
CZ B:ARG184 4.3 20.4 1.0
O4' C:DA4 4.3 26.9 1.0
O B:HOH604 4.4 21.9 1.0
O C:HOH602 4.4 14.2 0.9
C1' C:DC3 4.4 27.4 1.0
CZ B:TYR156 4.5 12.1 1.0
O B:HOH605 4.5 33.5 1.0
C3' C:DA4 4.5 22.6 1.0
CD B:ARG184 4.7 20.2 1.0
C2' C:DA4 4.7 25.5 1.0
O5' C:DC3 4.8 35.1 1.0
O4' C:DC3 4.8 29.6 1.0
N9 C:DA4 4.8 17.2 1.0
C5' C:DC3 4.8 31.5 1.0
N7 C:DA4 4.9 18.0 1.0
C1' C:DA4 4.9 22.2 1.0
CD2 B:TYR156 4.9 15.2 1.0

Phosphorus binding site 4 out of 40 in 1akh

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Phosphorus binding site 4 out of 40 in the Mat A1/ALPHA2/Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Mat A1/ALPHA2/Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P5

b:34.3
occ:1.00
 P C:DT5 0.0 34.3 1.0
OP1 C:DT5 1.5 26.8 1.0
OP2 C:DT5 1.5 33.6 1.0
O5' C:DT5 1.6 33.9 1.0
O3' C:DA4 1.6 24.7 1.0
C5' C:DT5 2.5 30.6 1.0
C3' C:DA4 2.6 22.6 1.0
C2' C:DA4 3.2 25.5 1.0
O C:HOH606 3.8 35.8 1.0
C4' C:DT5 3.8 26.4 1.0
C4' C:DA4 3.9 25.7 1.0
NZ B:LYS188 3.9 49.8 1.0
C1' C:DA4 4.1 22.2 1.0
O4' C:DT5 4.3 27.6 1.0
C3' C:DT5 4.4 23.7 1.0
O4' C:DA4 4.5 26.9 1.0
C2' C:DT5 4.8 20.7 1.0
CE B:LYS188 4.9 45.2 1.0

Phosphorus binding site 5 out of 40 in 1akh

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Phosphorus binding site 5 out of 40 in the Mat A1/ALPHA2/Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Mat A1/ALPHA2/Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P6

b:36.6
occ:1.00
 P C:DG6 0.0 36.6 1.0
OP2 C:DG6 1.5 40.6 1.0
OP1 C:DG6 1.5 40.8 1.0
O5' C:DG6 1.6 38.9 1.0
O3' C:DT5 1.6 31.7 1.0
C5' C:DG6 2.6 31.8 1.0
C3' C:DT5 2.6 23.7 1.0
C2' C:DT5 3.4 20.7 1.0
C4' C:DT5 3.8 26.4 1.0
C4' C:DG6 3.9 34.5 1.0
C1' C:DT5 4.3 21.1 1.0
C3' C:DG6 4.4 32.9 1.0
O4' C:DT5 4.7 27.6 1.0
O4' C:DG6 4.8 31.7 1.0
C5' C:DT5 4.9 30.6 1.0

Phosphorus binding site 6 out of 40 in 1akh

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Phosphorus binding site 6 out of 40 in the Mat A1/ALPHA2/Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Mat A1/ALPHA2/Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P7

b:48.0
occ:1.00
 P C:DT7 0.0 48.0 1.0
OP1 C:DT7 1.5 46.6 1.0
OP2 C:DT7 1.5 42.7 1.0
O5' C:DT7 1.6 43.2 1.0
O3' C:DG6 1.6 41.7 1.0
C5' C:DT7 2.6 43.5 1.0
C3' C:DG6 2.7 32.9 1.0
C2' C:DG6 3.1 33.2 1.0
C4' C:DT7 3.9 38.3 1.0
C4' C:DG6 4.0 34.5 1.0
C1' C:DG6 4.2 18.7 1.0
O4' C:DT7 4.3 40.7 1.0
C3' C:DT7 4.3 40.8 1.0
C2' C:DT7 4.5 38.2 1.0
C6 C:DT7 4.6 19.9 1.0
O4' C:DG6 4.7 31.7 1.0
C1' C:DT7 4.9 30.2 1.0

Phosphorus binding site 7 out of 40 in 1akh

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Phosphorus binding site 7 out of 40 in the Mat A1/ALPHA2/Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Mat A1/ALPHA2/Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P8

b:33.9
occ:1.00
 P C:DA8 0.0 33.9 1.0
OP1 C:DA8 1.5 44.9 1.0
OP2 C:DA8 1.5 38.8 1.0
O5' C:DA8 1.6 36.2 1.0
O3' C:DT7 1.6 44.4 1.0
C5' C:DA8 2.6 30.4 1.0
C3' C:DT7 2.7 40.8 1.0
C2' C:DT7 3.3 38.2 1.0
C4' C:DA8 3.9 33.5 1.0
C4' C:DT7 4.0 38.3 1.0
C1' C:DT7 4.1 30.2 1.0
C3' C:DA8 4.1 36.1 1.0
C2' C:DA8 4.4 28.4 1.0
O4' C:DT7 4.6 40.7 1.0
O4' C:DA8 4.7 32.5 1.0
C8 C:DA8 4.7 12.2 1.0

Phosphorus binding site 8 out of 40 in 1akh

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Phosphorus binding site 8 out of 40 in the Mat A1/ALPHA2/Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Mat A1/ALPHA2/Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P9

b:45.8
occ:1.00
 P C:DA9 0.0 45.8 1.0
OP1 C:DA9 1.5 40.2 1.0
OP2 C:DA9 1.5 31.7 1.0
O5' C:DA9 1.6 41.9 1.0
O3' C:DA8 1.6 42.4 1.0
C5' C:DA9 2.6 33.1 1.0
C3' C:DA8 2.6 36.1 1.0
C2' C:DA8 3.3 28.4 1.0
C4' C:DA8 3.9 33.5 1.0
C4' C:DA9 3.9 29.5 1.0
C1' C:DA8 4.1 22.5 1.0
C3' C:DA9 4.2 30.6 1.0
O4' C:DA9 4.3 34.7 1.0
C2' C:DA9 4.4 23.1 1.0
O4' C:DA8 4.4 32.5 1.0
NH1 B:ARG132 4.7 49.3 1.0
C1' C:DA9 4.9 24.7 1.0

Phosphorus binding site 9 out of 40 in 1akh

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Phosphorus binding site 9 out of 40 in the Mat A1/ALPHA2/Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Mat A1/ALPHA2/Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P10

b:41.7
occ:1.00
 P C:DA10 0.0 41.7 1.0
OP1 C:DA10 1.5 39.4 1.0
OP2 C:DA10 1.5 30.5 1.0
O5' C:DA10 1.6 36.4 1.0
O3' C:DA9 1.6 33.8 1.0
C5' C:DA10 2.6 35.3 1.0
C3' C:DA9 2.6 30.6 1.0
C2' C:DA9 3.4 23.1 1.0
C4' C:DA10 3.7 24.8 1.0
C4' C:DA9 3.9 29.5 1.0
O4' C:DA10 4.0 25.4 1.0
O C:HOH650 4.0 50.1 1.0
C1' C:DA9 4.3 24.7 1.0
O4' C:DA9 4.7 34.7 1.0
C5' C:DA9 4.9 33.1 1.0

Phosphorus binding site 10 out of 40 in 1akh

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Phosphorus binding site 10 out of 40 in the Mat A1/ALPHA2/Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Mat A1/ALPHA2/Dna Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P11

b:31.2
occ:1.00
 P C:DA11 0.0 31.2 1.0
OP2 C:DA11 1.5 32.8 1.0
OP1 C:DA11 1.5 28.2 1.0
O3' C:DA10 1.6 28.2 1.0
O5' C:DA11 1.6 34.8 1.0
C3' C:DA10 2.6 26.7 1.0
C5' C:DA11 2.6 26.0 1.0
C2' C:DA10 3.4 27.5 1.0
C4' C:DA10 3.8 24.8 1.0
C4' C:DA11 3.9 22.5 1.0
CE2 B:TYR131 4.0 10.7 1.0
OH B:TYR131 4.1 17.3 1.0
O C:HOH650 4.2 50.1 1.0
C3' C:DA11 4.3 20.6 1.0
O4' C:DA11 4.5 17.6 1.0
CZ B:TYR131 4.5 17.4 1.0
C2' C:DA11 4.5 12.6 1.0
C1' C:DA10 4.6 21.2 1.0
C5' C:DA10 4.6 35.3 1.0
O4' C:DA10 4.8 25.4 1.0

Reference:

T.Li, Y.Jin, A.K.Vershon, C.Wolberger. Crystal Structure of the MATA1/MATALPHA2 Homeodomain Heterodimer in Complex with Dna Containing An A-Tract. Nucleic Acids Res. V. 26 5707 1998.
ISSN: ISSN 0305-1048
PubMed: 9838003
DOI: 10.1093/NAR/26.24.5707
Page generated: Fri Sep 25 13:05:20 2020

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