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Zinc in PDB 1nwp: Crystallographic Study of Azurin From Pseudomonas Putida

Protein crystallography data

The structure of Crystallographic Study of Azurin From Pseudomonas Putida, PDB code: 1nwp was solved by F.S.Mathews, Z.-W.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.760, 51.220, 54.960, 90.00, 103.12, 90.00
R / Rfree (%) 18.1 / 24.8

Other elements in 1nwp:

The structure of Crystallographic Study of Azurin From Pseudomonas Putida also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystallographic Study of Azurin From Pseudomonas Putida (pdb code 1nwp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystallographic Study of Azurin From Pseudomonas Putida, PDB code: 1nwp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1nwp

Go back to Zinc Binding Sites List in 1nwp
Zinc binding site 1 out of 4 in the Crystallographic Study of Azurin From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystallographic Study of Azurin From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:18.7
occ:1.00
O A:HOH571 2.1 15.6 1.0
OD1 A:ASP23 2.2 10.7 1.0
OG A:SER25 2.2 15.6 1.0
O A:HOH653 2.3 17.5 1.0
CG A:ASP23 3.0 14.4 1.0
OD2 A:ASP23 3.2 15.8 1.0
CB A:SER25 3.3 16.7 1.0
N A:SER25 3.8 18.7 1.0
OXT A:LYS128 4.1 19.1 1.0
CA A:SER25 4.2 17.6 1.0
O A:LYS128 4.2 16.9 1.0
CB A:ASP23 4.5 14.0 1.0
N A:LYS24 4.5 14.2 1.0
C A:LYS128 4.6 19.6 1.0
C A:LYS24 4.9 17.9 1.0
CA A:ASP23 4.9 12.9 1.0
C A:ASP23 4.9 13.0 1.0

Zinc binding site 2 out of 4 in 1nwp

Go back to Zinc Binding Sites List in 1nwp
Zinc binding site 2 out of 4 in the Crystallographic Study of Azurin From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystallographic Study of Azurin From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:30.2
occ:1.00
O A:HOH713 1.9 33.6 1.0
O A:HOH618 2.0 30.2 1.0
NE2 A:HIS83 2.0 11.0 1.0
O A:HOH632 2.2 38.8 1.0
O A:HOH646 2.3 48.8 1.0
O A:HOH606 2.8 37.9 1.0
CE1 A:HIS83 3.0 8.6 1.0
CD2 A:HIS83 3.1 9.1 1.0
O A:HOH671 4.0 25.2 1.0
O A:HOH577 4.1 31.3 1.0
ND1 A:HIS83 4.1 10.4 1.0
CG A:HIS83 4.2 7.5 1.0
O A:HOH548 4.2 41.6 1.0
O A:HOH578 4.7 19.6 1.0
O A:HOH574 4.9 14.6 1.0

Zinc binding site 3 out of 4 in 1nwp

Go back to Zinc Binding Sites List in 1nwp
Zinc binding site 3 out of 4 in the Crystallographic Study of Azurin From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystallographic Study of Azurin From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:18.4
occ:1.00
NE2 B:HIS83 2.0 9.6 1.0
O B:HOH537 2.1 20.4 1.0
CD2 B:HIS83 2.9 11.6 1.0
CE1 B:HIS83 3.1 9.0 1.0
CG B:HIS83 4.1 9.4 1.0
O B:HOH538 4.1 36.5 1.0
ND1 B:HIS83 4.2 8.9 1.0
O B:HOH637 4.4 48.2 1.0
O B:HOH687 4.6 46.3 1.0
O B:HOH544 4.6 30.0 1.0
O B:HOH509 5.0 17.1 1.0

Zinc binding site 4 out of 4 in 1nwp

Go back to Zinc Binding Sites List in 1nwp
Zinc binding site 4 out of 4 in the Crystallographic Study of Azurin From Pseudomonas Putida


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystallographic Study of Azurin From Pseudomonas Putida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:32.1
occ:1.00
OD2 B:ASP62 2.1 20.3 1.0
O B:HOH525 2.3 20.9 1.0
CG B:ASP62 2.8 18.5 1.0
OD1 B:ASP62 2.8 22.2 1.0
NZ B:LYS74 3.8 33.7 1.0
O B:HOH680 4.1 32.4 1.0
CB B:ASP62 4.2 15.8 1.0
NH2 B:ARG79 4.3 12.9 1.0
CE B:LYS74 4.7 30.5 1.0
NH1 B:ARG79 4.7 13.5 1.0
CZ B:ARG79 4.9 15.2 1.0
CD B:LYS74 5.0 28.4 1.0

Reference:

Z.W.Chen, M.J.Barber, W.S.Mcintire, F.S.Mathews. Crystallographic Study of Azurin From Pseudomonas Putida. Acta Crystallogr.,Sect.D V. 54 253 1998.
ISSN: ISSN 0907-4449
PubMed: 9761890
DOI: 10.1107/S0907444997011505
Page generated: Mon Jan 25 16:10:42 2021

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