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Zinc in PDB 7wi1: The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination.

Enzymatic activity of The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination.

All present enzymatic activity of The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination.:
3.5.2.6;

Protein crystallography data

The structure of The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination., PDB code: 7wi1 was solved by Y.S.Park, L.W.Kang, J.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.51 / 1.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 121.755, 82.792, 164.047, 90, 111.1, 90
R / Rfree (%) 19.6 / 22.3

Zinc Binding Sites:

The binding sites of Zinc atom in the The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination. (pdb code 7wi1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination., PDB code: 7wi1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7wi1

Go back to Zinc Binding Sites List in 7wi1
Zinc binding site 1 out of 8 in the The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:11.1
occ:1.00
 O A:HOH523 2.1 10.9 1.0
NE2 A:HIS96 2.1 8.8 1.0
NE2 A:HIS279 2.1 9.9 1.0
OD2 A:ASP210 2.1 10.9 1.0
OD2 A:ASP95 2.2 12.4 1.0
CD2 A:HIS96 3.0 7.1 1.0
CE1 A:HIS279 3.0 9.8 1.0
CG A:ASP210 3.0 14.1 1.0
CD2 A:HIS279 3.1 10.8 1.0
CE1 A:HIS96 3.1 8.2 1.0
O A:HOH502 3.2 0.5 1.0
CG A:ASP95 3.2 11.3 1.0
OD1 A:ASP210 3.2 14.8 1.0
OD1 A:ASP95 3.5 13.4 1.0
O A:HOH566 3.8 40.8 1.0
O A:HOH598 3.9 13.3 1.0
NE2 A:HIS91 4.0 7.1 1.0
CE1 A:HIS91 4.1 7.2 1.0
ND1 A:HIS279 4.1 11.7 1.0
CG A:HIS96 4.2 8.2 1.0
CG A:HIS279 4.2 9.6 1.0
ND1 A:HIS96 4.2 7.9 1.0
CB A:ASP210 4.4 13.5 1.0
CB A:ASP95 4.5 10.3 1.0
NE2 A:HIS188 4.7 14.7 1.0

Zinc binding site 2 out of 8 in 7wi1

Go back to Zinc Binding Sites List in 7wi1
Zinc binding site 2 out of 8 in the The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn401

b:10.8
occ:1.00
 NE2 G:HIS96 1.9 5.5 1.0
O G:HOH530 2.0 10.2 1.0
NE2 G:HIS279 2.0 10.3 1.0
OD2 G:ASP210 2.1 9.8 1.0
OD2 G:ASP95 2.3 9.9 1.0
CD2 G:HIS96 2.9 6.6 1.0
CE1 G:HIS279 3.0 11.1 1.0
CE1 G:HIS96 3.0 6.7 1.0
CG G:ASP210 3.0 13.0 1.0
CD2 G:HIS279 3.0 10.5 1.0
O G:HOH502 3.2 0.5 1.0
CG G:ASP95 3.2 10.9 1.0
OD1 G:ASP210 3.3 14.2 1.0
OD1 G:ASP95 3.5 10.0 1.0
O G:HOH582 3.9 32.0 1.0
O G:HOH569 4.0 12.3 1.0
NE2 G:HIS91 4.0 8.3 1.0
CG G:HIS96 4.1 6.6 1.0
ND1 G:HIS96 4.1 6.5 1.0
ND1 G:HIS279 4.1 10.6 1.0
CE1 G:HIS91 4.1 8.2 1.0
CG G:HIS279 4.2 10.6 1.0
CB G:ASP210 4.4 12.0 1.0
CB G:ASP95 4.6 9.0 1.0
NE2 G:HIS188 4.8 13.2 1.0
O G:HOH576 5.0 15.2 1.0

Zinc binding site 3 out of 8 in 7wi1

Go back to Zinc Binding Sites List in 7wi1
Zinc binding site 3 out of 8 in the The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:7.9
occ:1.00
 NE2 C:HIS279 2.0 7.3 1.0
OD2 C:ASP210 2.0 9.8 1.0
NE2 C:HIS96 2.0 3.6 1.0
O C:HOH522 2.1 10.4 1.0
OD2 C:ASP95 2.3 9.3 1.0
CE1 C:HIS279 2.9 8.6 1.0
CD2 C:HIS96 3.0 4.3 1.0
CG C:ASP210 3.0 8.8 1.0
CD2 C:HIS279 3.0 8.0 1.0
CE1 C:HIS96 3.1 4.3 1.0
O C:HOH502 3.2 0.5 1.0
CG C:ASP95 3.2 7.9 1.0
OD1 C:ASP210 3.2 9.8 1.0
OD1 C:ASP95 3.5 7.7 1.0
O C:HOH598 3.8 19.2 1.0
O C:HOH586 3.9 9.6 1.0
ND1 C:HIS279 4.1 8.8 1.0
NE2 C:HIS91 4.1 3.8 1.0
CG C:HIS96 4.1 4.1 1.0
CG C:HIS279 4.1 7.4 1.0
ND1 C:HIS96 4.1 4.2 1.0
CE1 C:HIS91 4.2 4.1 1.0
CB C:ASP210 4.4 8.2 1.0
CB C:ASP95 4.6 7.2 1.0
NE2 C:HIS188 4.8 9.1 1.0

Zinc binding site 4 out of 8 in 7wi1

Go back to Zinc Binding Sites List in 7wi1
Zinc binding site 4 out of 8 in the The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:8.5
occ:1.00
 NE2 E:HIS279 2.0 7.3 1.0
OD2 E:ASP95 2.0 8.0 1.0
NE2 E:HIS96 2.1 3.8 1.0
OD2 E:ASP210 2.1 8.4 1.0
O E:HOH512 2.2 13.0 1.0
CE1 E:HIS279 2.9 7.3 1.0
CG E:ASP210 3.0 8.5 1.0
CD2 E:HIS96 3.0 4.3 1.0
CD2 E:HIS279 3.0 7.7 1.0
CE1 E:HIS96 3.1 4.5 1.0
CG E:ASP95 3.1 7.4 1.0
OD1 E:ASP210 3.2 10.6 1.0
O E:HOH503 3.2 0.5 1.0
OD1 E:ASP95 3.5 7.4 1.0
O E:HOH565 3.9 22.2 1.0
O E:HOH544 3.9 8.1 1.0
ND1 E:HIS279 4.1 7.6 1.0
NE2 E:HIS91 4.1 4.2 1.0
CG E:HIS279 4.1 7.3 1.0
CG E:HIS96 4.1 4.2 1.0
CE1 E:HIS91 4.2 4.3 1.0
ND1 E:HIS96 4.2 4.3 1.0
CB E:ASP210 4.4 8.1 1.0
CB E:ASP95 4.5 7.1 1.0
NE2 E:HIS188 4.9 10.5 1.0

Zinc binding site 5 out of 8 in 7wi1

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Zinc binding site 5 out of 8 in the The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:9.3
occ:1.00
 NE2 D:HIS96 2.0 5.7 1.0
O D:HOH535 2.1 10.1 1.0
NE2 D:HIS279 2.1 6.6 1.0
OD2 D:ASP210 2.1 8.2 1.0
OD2 D:ASP95 2.2 9.1 1.0
CD2 D:HIS96 2.9 5.2 1.0
CG D:ASP210 3.0 9.9 1.0
CE1 D:HIS279 3.0 7.3 1.0
CD2 D:HIS279 3.1 7.3 1.0
CE1 D:HIS96 3.1 5.2 1.0
O D:HOH502 3.2 0.5 1.0
CG D:ASP95 3.2 7.8 1.0
OD1 D:ASP210 3.2 11.4 1.0
OD1 D:ASP95 3.5 7.1 1.0
O D:HOH641 3.9 24.8 1.0
O D:HOH619 4.0 9.7 1.0
NE2 D:HIS91 4.1 5.2 1.0
CG D:HIS96 4.1 5.2 1.0
CE1 D:HIS91 4.1 5.2 1.0
ND1 D:HIS96 4.1 5.6 1.0
ND1 D:HIS279 4.2 8.0 1.0
CG D:HIS279 4.2 7.4 1.0
CB D:ASP210 4.4 9.8 1.0
CB D:ASP95 4.5 7.0 1.0
NE2 D:HIS188 4.8 10.3 1.0

Zinc binding site 6 out of 8 in 7wi1

Go back to Zinc Binding Sites List in 7wi1
Zinc binding site 6 out of 8 in the The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:8.5
occ:1.00
 O F:HOH506 1.9 9.4 1.0
NE2 F:HIS96 2.0 5.3 1.0
OD2 F:ASP210 2.1 8.7 1.0
NE2 F:HIS279 2.1 6.2 1.0
OD2 F:ASP95 2.3 9.2 1.0
CD2 F:HIS96 2.9 5.2 1.0
CG F:ASP210 3.0 10.2 1.0
CE1 F:HIS279 3.0 6.8 1.0
CD2 F:HIS279 3.1 6.7 1.0
CE1 F:HIS96 3.1 5.4 1.0
O F:HOH502 3.2 0.5 1.0
CG F:ASP95 3.2 7.8 1.0
OD1 F:ASP210 3.3 11.0 1.0
OD1 F:ASP95 3.5 7.8 1.0
O F:HOH573 3.8 21.7 1.0
O F:HOH564 4.0 8.4 1.0
CG F:HIS96 4.1 5.3 1.0
NE2 F:HIS91 4.1 5.0 1.0
ND1 F:HIS279 4.1 7.1 1.0
ND1 F:HIS96 4.1 5.5 1.0
CE1 F:HIS91 4.1 5.3 1.0
CG F:HIS279 4.2 6.4 1.0
CB F:ASP210 4.4 10.0 1.0
CB F:ASP95 4.5 6.7 1.0
NE2 F:HIS188 4.8 8.7 1.0

Zinc binding site 7 out of 8 in 7wi1

Go back to Zinc Binding Sites List in 7wi1
Zinc binding site 7 out of 8 in the The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:9.3
occ:1.00
 OD2 B:ASP95 2.0 11.4 1.0
NE2 B:HIS279 2.0 8.3 1.0
O B:HOH508 2.0 11.5 1.0
NE2 B:HIS96 2.1 5.2 1.0
OD2 B:ASP210 2.1 9.7 1.0
CD2 B:HIS96 2.9 5.2 1.0
CG B:ASP210 3.0 11.4 1.0
CD2 B:HIS279 3.0 8.1 1.0
CE1 B:HIS279 3.0 8.1 1.0
CG B:ASP95 3.1 9.4 1.0
CE1 B:HIS96 3.2 5.5 1.0
OD1 B:ASP210 3.2 13.4 1.0
O B:HOH502 3.2 0.5 1.0
OD1 B:ASP95 3.5 8.7 1.0
O B:HOH622 4.0 10.3 1.0
NE2 B:HIS91 4.1 5.7 1.0
ND1 B:HIS279 4.1 8.2 1.0
CG B:HIS96 4.1 5.8 1.0
O B:HOH651 4.1 26.8 1.0
CG B:HIS279 4.1 8.2 1.0
CE1 B:HIS91 4.1 7.0 1.0
ND1 B:HIS96 4.2 5.3 1.0
CB B:ASP210 4.4 10.0 1.0
CB B:ASP95 4.4 8.5 1.0
NE2 B:HIS188 4.8 12.9 1.0

Zinc binding site 8 out of 8 in 7wi1

Go back to Zinc Binding Sites List in 7wi1
Zinc binding site 8 out of 8 in the The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Mutant Variant of Pngm-1. H279A Was Substituted For Alanine to Study Metal Coordination. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn401

b:9.1
occ:1.00
 O H:HOH507 2.0 9.0 1.0
OD2 H:ASP210 2.0 12.1 1.0
NE2 H:HIS96 2.1 5.1 1.0
NE2 H:HIS279 2.1 7.7 1.0
OD2 H:ASP95 2.3 9.2 1.0
CD2 H:HIS96 2.9 5.0 1.0
CG H:ASP210 2.9 10.4 1.0
CE1 H:HIS279 3.0 8.3 1.0
CD2 H:HIS279 3.1 7.6 1.0
CE1 H:HIS96 3.2 5.7 1.0
O H:HOH503 3.2 0.5 1.0
OD1 H:ASP210 3.2 11.6 1.0
CG H:ASP95 3.2 9.4 1.0
OD1 H:ASP95 3.5 9.6 1.0
O H:HOH575 3.9 29.6 1.0
O H:HOH562 3.9 10.3 1.0
NE2 H:HIS91 4.1 5.7 1.0
CG H:HIS96 4.1 5.4 1.0
ND1 H:HIS279 4.2 8.2 1.0
ND1 H:HIS96 4.2 5.5 1.0
CE1 H:HIS91 4.2 5.7 1.0
CG H:HIS279 4.2 7.7 1.0
CB H:ASP210 4.4 9.8 1.0
CB H:ASP95 4.5 7.8 1.0
NE2 H:HIS188 4.7 10.8 1.0
O H:ASP95 5.0 6.4 1.0

Reference:

Y.S.Park, L.W.Kang, J.H.Lee. Structural Study of Metal Binding and Coordination of Ancient Metallo Beta Lactamase Pngm 1 Variants To Be Published.
Page generated: Fri Aug 22 06:15:00 2025

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