Phosphorus in PDB 1afl: Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution

Enzymatic activity of Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution

All present enzymatic activity of Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution:
3.1.27.5;

Protein crystallography data

The structure of Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution, PDB code: 1afl was solved by D.D.Leonidas, K.R.Acharya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.930, 33.440, 73.690, 90.00, 90.08, 90.00
R / Rfree (%) 21.7 / 27.8

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution (pdb code 1afl). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 6 binding sites of Phosphorus where determined in the Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution, PDB code: 1afl:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6;

Phosphorus binding site 1 out of 6 in 1afl

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Phosphorus binding site 1 out of 6 in the Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P125

b:29.3
occ:1.00
 PB A:ATR125 0.0 29.3 1.0
O1B A:ATR125 1.5 30.2 1.0
O3B A:ATR125 1.5 30.2 1.0
O2B A:ATR125 1.5 26.9 1.0
O3A A:ATR125 1.6 37.4 1.0
PA A:ATR125 3.1 47.6 1.0
C5' A:ATR125 3.5 45.5 1.0
O A:HOH1024 3.6 17.2 1.0
O5' A:ATR125 3.6 45.6 1.0
ND1 A:HIS119 3.6 26.9 1.0
NE2 A:HIS12 3.7 9.9 1.0
O2A A:ATR125 3.7 45.7 1.0
NE2 A:GLN11 3.9 20.1 1.0
N A:PHE120 4.1 12.5 1.0
O1A A:ATR125 4.1 45.3 1.0
CE1 A:HIS119 4.4 26.5 1.0
CG A:HIS119 4.4 22.6 1.0
CA A:HIS119 4.4 13.0 1.0
CE1 A:HIS12 4.4 9.5 1.0
O A:PHE120 4.5 12.8 1.0
CB A:HIS119 4.5 16.0 1.0
NZ A:LYS41 4.6 32.1 1.0
CD2 A:HIS12 4.8 10.2 1.0
C A:HIS119 4.8 12.5 1.0
C4' A:ATR125 4.8 44.9 1.0
CD A:GLN11 4.9 19.5 1.0

Phosphorus binding site 2 out of 6 in 1afl

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Phosphorus binding site 2 out of 6 in the Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P125

b:47.6
occ:1.00
 PA A:ATR125 0.0 47.6 1.0
O1A A:ATR125 1.5 45.3 1.0
O2A A:ATR125 1.5 45.7 1.0
O5' A:ATR125 1.7 45.6 1.0
O3A A:ATR125 1.7 37.4 1.0
C5' A:ATR125 2.5 45.5 1.0
PB A:ATR125 3.1 29.3 1.0
NZ A:LYS7 3.2 35.5 1.0
C4' A:ATR125 3.3 44.9 1.0
O3B A:ATR125 3.5 30.2 1.0
O1B A:ATR125 3.6 30.2 1.0
NE2 A:GLN11 3.9 20.1 1.0
O2B A:ATR125 4.0 26.9 1.0
C3' A:ATR125 4.1 46.1 1.0
O A:HOH1024 4.2 17.2 1.0
O3' A:ATR125 4.3 46.8 1.0
O A:HOH1060 4.3 34.3 1.0
O4' A:ATR125 4.4 44.3 1.0
CE A:LYS7 4.5 31.0 1.0
O A:HOH1025 4.7 23.2 1.0
CD A:GLN11 4.9 19.5 1.0
CD A:LYS7 4.9 25.0 1.0

Phosphorus binding site 3 out of 6 in 1afl

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Phosphorus binding site 3 out of 6 in the Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P125

b:55.8
occ:1.00
 P2' A:ATR125 0.0 55.8 1.0
O1P A:ATR125 1.5 53.2 1.0
O3P A:ATR125 1.5 53.5 1.0
O2P A:ATR125 1.5 54.0 1.0
O2' A:ATR125 1.6 51.7 1.0
C2' A:ATR125 2.6 46.8 1.0
OE1 A:GLU111 3.0 23.1 1.0
C1' A:ATR125 3.1 42.8 1.0
O A:HOH1051 3.2 48.0 1.0
O A:HOH1038 3.3 44.0 1.0
O A:HOH1028 3.6 36.9 1.0
CD A:GLU111 3.7 22.0 1.0
C8 A:ATR125 3.8 39.1 1.0
N9 A:ATR125 3.8 40.9 1.0
C3' A:ATR125 3.9 46.1 1.0
CG2 A:VAL118 4.0 10.7 1.0
OE2 A:GLU111 4.1 25.8 1.0
CB A:ALA4 4.1 22.4 1.0
O3' A:ATR125 4.1 46.8 1.0
CB A:VAL118 4.2 11.2 1.0
O4' A:ATR125 4.2 44.3 1.0
C4' A:ATR125 4.4 44.9 1.0
CG1 A:VAL118 4.6 10.8 1.0
CG A:GLU111 4.8 17.7 1.0

Phosphorus binding site 4 out of 6 in 1afl

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Phosphorus binding site 4 out of 6 in the Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P125

b:30.8
occ:1.00
 PB B:ATR125 0.0 30.8 1.0
O1B B:ATR125 1.5 33.1 1.0
O2B B:ATR125 1.5 28.9 1.0
O3B B:ATR125 1.5 33.1 1.0
O3A B:ATR125 1.6 35.9 1.0
PA B:ATR125 3.1 45.8 1.0
O B:HOH1004 3.4 13.4 1.0
ND1 B:HIS119 3.5 28.9 1.0
O2A B:ATR125 3.5 44.2 1.0
O B:HOH1038 3.6 27.6 1.0
NE2 B:HIS12 3.8 8.6 1.0
NE2 B:GLN11 3.8 13.8 1.0
O5' B:ATR125 3.9 44.1 1.0
N B:PHE120 4.0 9.9 1.0
CE1 B:HIS119 4.1 30.2 1.0
O1A B:ATR125 4.1 45.1 1.0
C5' B:ATR125 4.2 41.3 1.0
CG B:HIS119 4.3 25.2 1.0
CA B:HIS119 4.3 11.3 1.0
O B:PHE120 4.5 11.7 1.0
CB B:HIS119 4.6 17.5 1.0
CE1 B:HIS12 4.6 6.4 1.0
C B:HIS119 4.7 10.0 1.0
CD2 B:HIS12 4.8 7.6 1.0
NZ B:LYS7 4.8 31.7 1.0
CD B:GLN11 4.9 14.6 1.0
O B:HOH1052 5.0 54.3 1.0
CA B:PHE120 5.0 10.6 1.0

Phosphorus binding site 5 out of 6 in 1afl

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Phosphorus binding site 5 out of 6 in the Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P125

b:45.8
occ:1.00
 PA B:ATR125 0.0 45.8 1.0
O1A B:ATR125 1.5 45.1 1.0
O2A B:ATR125 1.5 44.2 1.0
O5' B:ATR125 1.7 44.1 1.0
O3A B:ATR125 1.7 35.9 1.0
C5' B:ATR125 2.5 41.3 1.0
PB B:ATR125 3.1 30.8 1.0
NZ B:LYS7 3.3 31.7 1.0
C4' B:ATR125 3.4 41.0 1.0
O1B B:ATR125 3.6 33.1 1.0
O B:HOH1003 3.6 23.3 1.0
O3B B:ATR125 3.6 33.1 1.0
O B:HOH1004 3.9 13.4 1.0
O2B B:ATR125 4.0 28.9 1.0
ND1 B:HIS119 4.3 28.9 1.0
C3' B:ATR125 4.4 44.2 1.0
O B:VAL118 4.4 12.8 1.0
O3' B:ATR125 4.4 43.8 1.0
O4' B:ATR125 4.4 42.3 1.0
CE B:LYS7 4.5 24.6 1.0
NE2 B:GLN11 4.5 13.8 1.0
CD B:LYS7 4.7 21.9 1.0
CB B:HIS119 4.9 17.5 1.0

Phosphorus binding site 6 out of 6 in 1afl

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Phosphorus binding site 6 out of 6 in the Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Ribonuclease A in Complex with 5'-Diphosphoadenosine 2'- Phosphate at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P125

b:54.2
occ:1.00
 P2' B:ATR125 0.0 54.2 1.0
O3P B:ATR125 1.5 52.5 1.0
O1P B:ATR125 1.5 51.2 1.0
O2P B:ATR125 1.5 52.7 1.0
O2' B:ATR125 1.7 49.4 1.0
C2' B:ATR125 2.8 44.8 1.0
C1' B:ATR125 3.3 42.8 1.0
OE2 B:GLU111 3.4 35.1 1.0
OE1 B:GLU111 3.5 35.1 1.0
CD B:GLU111 3.6 30.3 1.0
N9 B:ATR125 4.1 38.6 1.0
C8 B:ATR125 4.2 36.8 1.0
C3' B:ATR125 4.2 44.2 1.0
CB B:ALA4 4.2 18.8 1.0
O4' B:ATR125 4.4 42.3 1.0
CG2 B:VAL118 4.5 14.0 1.0
C4' B:ATR125 4.7 41.0 1.0
O3' B:ATR125 4.7 43.8 1.0
CG B:GLU111 4.7 25.1 1.0
CB B:VAL118 4.8 12.4 1.0
CB B:GLU111 4.9 16.4 1.0

Reference:

D.D.Leonidas, R.Shapiro, L.I.Irons, N.Russo, K.R.Acharya. Crystal Structures of Ribonuclease A Complexes with 5'-Diphosphoadenosine 3'-Phosphate and 5'-Diphosphoadenosine 2'-Phosphate at 1.7 A Resolution. Biochemistry V. 36 5578 1997.
ISSN: ISSN 0006-2960
PubMed: 9154942
DOI: 10.1021/BI9700330
Page generated: Fri Sep 25 12:48:05 2020

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