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

Go back to Phosphorus Binding Sites List in 1afl
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

Go back to Phosphorus Binding Sites List in 1afl
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

Go back to Phosphorus Binding Sites List in 1afl
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

Go back to Phosphorus Binding Sites List in 1afl
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

Go back to Phosphorus Binding Sites List in 1afl
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

Go back to Phosphorus Binding Sites List in 1afl
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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy