Atomistry » Zinc » PDB 7bq7-7c2o » 7bz3
Atomistry »
  Zinc »
    PDB 7bq7-7c2o »
      7bz3 »

Zinc in PDB 7bz3: The Mutant Variant of Pngm-1. H257 Was Substituted For Alanine to Study Substrate Binding.

Enzymatic activity of The Mutant Variant of Pngm-1. H257 Was Substituted For Alanine to Study Substrate Binding.

All present enzymatic activity of The Mutant Variant of Pngm-1. H257 Was Substituted For Alanine to Study Substrate Binding.:
3.5.2.6;

Protein crystallography data

The structure of The Mutant Variant of Pngm-1. H257 Was Substituted For Alanine to Study Substrate Binding., PDB code: 7bz3 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) 48.69 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.787, 143.741, 79.76, 90, 111.82, 90
R / Rfree (%) 22.9 / 28.6

Zinc Binding Sites:

The binding sites of Zinc atom in the The Mutant Variant of Pngm-1. H257 Was Substituted For Alanine to Study Substrate Binding. (pdb code 7bz3). 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. H257 Was Substituted For Alanine to Study Substrate Binding., PDB code: 7bz3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7bz3

Go back to Zinc Binding Sites List in 7bz3
Zinc binding site 1 out of 8 in the The Mutant Variant of Pngm-1. H257 Was Substituted For Alanine to Study Substrate Binding.


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. H257 Was Substituted For Alanine to Study Substrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:17.4
occ:1.00
 O A:HOH509 1.9 11.7 1.0
NE2 A:HIS279 2.0 13.4 1.0
NE2 A:HIS96 2.1 12.2 1.0
OD2 A:ASP210 2.1 16.8 1.0
OD2 A:ASP95 2.2 15.1 1.0
CG A:ASP210 2.9 17.7 1.0
CD2 A:HIS96 3.0 13.0 1.0
CE1 A:HIS279 3.0 15.4 1.0
CD2 A:HIS279 3.0 14.1 1.0
OD1 A:ASP210 3.1 18.0 1.0
CG A:ASP95 3.1 14.3 1.0
CE1 A:HIS96 3.2 13.5 1.0
ZN A:ZN402 3.3 16.9 1.0
OD1 A:ASP95 3.5 15.8 1.0
O A:HOH517 3.6 38.5 1.0
ND1 A:HIS279 4.1 14.8 1.0
O A:HOH595 4.1 18.7 1.0
CG A:HIS279 4.2 14.9 1.0
CG A:HIS96 4.2 13.2 1.0
CE1 A:HIS91 4.2 21.0 1.0
NE2 A:HIS91 4.2 20.4 1.0
ND1 A:HIS96 4.2 12.9 1.0
CB A:ASP210 4.3 17.4 1.0
CB A:ASP95 4.5 14.6 1.0
NE2 A:HIS188 4.9 16.6 1.0
ND1 A:HIS93 5.0 16.6 1.0

Zinc binding site 2 out of 8 in 7bz3

Go back to Zinc Binding Sites List in 7bz3
Zinc binding site 2 out of 8 in the The Mutant Variant of Pngm-1. H257 Was Substituted For Alanine to Study Substrate Binding.


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. H257 Was Substituted For Alanine to Study Substrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:16.9
occ:1.00
 O A:HOH509 1.9 11.7 1.0
NE2 A:HIS188 2.1 16.6 1.0
ND1 A:HIS93 2.2 16.6 1.0
NE2 A:HIS91 2.2 20.4 1.0
OD2 A:ASP210 2.5 16.8 1.0
CE1 A:HIS188 3.0 15.6 1.0
CE1 A:HIS93 3.0 17.4 1.0
CD2 A:HIS188 3.1 16.9 1.0
CD2 A:HIS91 3.1 20.5 1.0
CE1 A:HIS91 3.1 21.0 1.0
CG A:HIS93 3.2 17.2 1.0
ZN A:ZN401 3.3 17.4 1.0
CG A:ASP210 3.4 17.7 1.0
CB A:HIS93 3.6 17.3 1.0
CB A:ASP210 3.8 17.4 1.0
NE2 A:HIS96 3.8 12.2 1.0
O A:HOH517 3.9 38.5 1.0
CD2 A:HIS96 4.0 13.0 1.0
ND1 A:HIS188 4.1 16.6 1.0
CG A:HIS188 4.2 16.5 1.0
NE2 A:HIS93 4.2 17.1 1.0
OD1 A:ASP95 4.2 15.8 1.0
ND1 A:HIS91 4.2 18.5 1.0
CG A:HIS91 4.3 20.0 1.0
CD2 A:HIS93 4.3 17.8 1.0
OD1 A:ASP210 4.4 18.0 1.0
OD2 A:ASP95 4.6 15.1 1.0
CG A:ASP95 4.9 14.3 1.0
CE1 A:HIS96 4.9 13.5 1.0
CA A:HIS93 4.9 16.9 1.0
NE2 A:HIS279 5.0 13.4 1.0

Zinc binding site 3 out of 8 in 7bz3

Go back to Zinc Binding Sites List in 7bz3
Zinc binding site 3 out of 8 in the The Mutant Variant of Pngm-1. H257 Was Substituted For Alanine to Study Substrate Binding.


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. H257 Was Substituted For Alanine to Study Substrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:17.7
occ:1.00
 O B:HOH513 1.9 14.1 1.0
NE2 B:HIS279 2.0 19.8 1.0
NE2 B:HIS96 2.1 17.7 1.0
OD2 B:ASP210 2.1 13.9 1.0
OD2 B:ASP95 2.2 17.0 1.0
CE1 B:HIS279 2.9 20.2 1.0
CD2 B:HIS96 2.9 17.4 1.0
CG B:ASP210 2.9 15.8 1.0
OD1 B:ASP210 3.0 19.6 1.0
CD2 B:HIS279 3.1 19.6 1.0
CE1 B:HIS96 3.2 15.3 1.0
CG B:ASP95 3.2 18.1 1.0
ZN B:ZN402 3.4 18.8 1.0
OD1 B:ASP95 3.6 21.5 1.0
NE2 B:HIS91 4.0 15.2 1.0
ND1 B:HIS279 4.1 20.2 1.0
CG B:HIS96 4.1 18.2 1.0
CE1 B:HIS91 4.1 15.3 1.0
ND1 B:HIS96 4.2 16.9 1.0
CG B:HIS279 4.2 18.9 1.0
O B:HOH560 4.2 15.2 1.0
CB B:ASP210 4.4 16.4 1.0
CB B:ASP95 4.5 19.3 1.0
NE2 B:HIS188 4.9 16.6 1.0
O B:ASP95 5.0 18.5 1.0

Zinc binding site 4 out of 8 in 7bz3

Go back to Zinc Binding Sites List in 7bz3
Zinc binding site 4 out of 8 in the The Mutant Variant of Pngm-1. H257 Was Substituted For Alanine to Study Substrate Binding.


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. H257 Was Substituted For Alanine to Study Substrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:18.8
occ:1.00
 NE2 B:HIS188 2.1 16.6 1.0
NE2 B:HIS91 2.1 15.2 1.0
O B:HOH513 2.1 14.1 1.0
ND1 B:HIS93 2.2 14.9 1.0
OD2 B:ASP210 2.5 13.9 1.0
CD2 B:HIS91 2.9 17.2 1.0
CD2 B:HIS188 2.9 16.5 1.0
CE1 B:HIS93 3.0 17.5 1.0
CE1 B:HIS188 3.0 14.8 1.0
CE1 B:HIS91 3.2 15.3 1.0
CG B:HIS93 3.2 15.8 1.0
CG B:ASP210 3.4 15.8 1.0
ZN B:ZN401 3.4 17.7 1.0
CB B:HIS93 3.6 16.8 1.0
CB B:ASP210 3.8 16.4 1.0
CG B:HIS188 4.0 16.9 1.0
NE2 B:HIS96 4.1 17.7 1.0
ND1 B:HIS188 4.1 16.7 1.0
CD2 B:HIS96 4.1 17.4 1.0
CG B:HIS91 4.1 16.1 1.0
ND1 B:HIS91 4.2 15.5 1.0
NE2 B:HIS93 4.2 16.2 1.0
CD2 B:HIS93 4.3 16.3 1.0
OD1 B:ASP95 4.3 21.5 1.0
OD1 B:ASP210 4.4 19.6 1.0
OD2 B:ASP95 4.7 17.0 1.0
CG B:ASP95 4.9 18.1 1.0
CA B:HIS93 5.0 17.0 1.0

Zinc binding site 5 out of 8 in 7bz3

Go back to Zinc Binding Sites List in 7bz3
Zinc binding site 5 out of 8 in the The Mutant Variant of Pngm-1. H257 Was Substituted For Alanine to Study Substrate Binding.


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. H257 Was Substituted For Alanine to Study Substrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:22.6
occ:1.00
 NE2 C:HIS279 1.9 30.7 1.0
O C:HOH549 1.9 12.8 1.0
NE2 C:HIS96 2.0 18.6 1.0
OD2 C:ASP210 2.2 23.2 1.0
OD2 C:ASP95 2.4 20.6 1.0
CE1 C:HIS279 2.5 33.6 1.0
CD2 C:HIS96 2.9 18.3 1.0
CG C:ASP210 3.0 22.6 1.0
CE1 C:HIS96 3.0 18.7 1.0
OD1 C:ASP210 3.1 21.9 1.0
CD2 C:HIS279 3.2 31.1 1.0
CG C:ASP95 3.3 20.9 1.0
ZN C:ZN402 3.3 19.5 1.0
OD1 C:ASP95 3.6 22.7 1.0
ND1 C:HIS279 3.7 35.2 1.0
CG C:HIS279 4.1 30.1 1.0
CG C:HIS96 4.1 18.5 1.0
ND1 C:HIS96 4.1 18.9 1.0
NE2 C:HIS91 4.2 18.0 1.0
CE1 C:HIS91 4.2 20.1 1.0
CB C:ASP210 4.4 20.8 1.0
CB C:ASP95 4.6 20.7 1.0
O C:HOH503 4.6 39.7 1.0
O C:HOH530 4.6 33.7 1.0
NE2 C:HIS188 5.0 21.6 1.0

Zinc binding site 6 out of 8 in 7bz3

Go back to Zinc Binding Sites List in 7bz3
Zinc binding site 6 out of 8 in the The Mutant Variant of Pngm-1. H257 Was Substituted For Alanine to Study Substrate Binding.


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. H257 Was Substituted For Alanine to Study Substrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:19.5
occ:1.00
 NE2 C:HIS91 2.1 18.0 1.0
ND1 C:HIS93 2.2 18.3 1.0
O C:HOH549 2.2 12.8 1.0
NE2 C:HIS188 2.2 21.6 1.0
OD2 C:ASP210 2.3 23.2 1.0
CD2 C:HIS91 3.1 17.9 1.0
CE1 C:HIS93 3.1 19.7 1.0
CE1 C:HIS91 3.1 20.1 1.0
CD2 C:HIS188 3.1 22.1 1.0
CE1 C:HIS188 3.1 25.2 1.0
CG C:HIS93 3.1 19.4 1.0
ZN C:ZN401 3.3 22.6 1.0
CG C:ASP210 3.4 22.6 1.0
CB C:HIS93 3.5 17.8 1.0
NE2 C:HIS96 3.9 18.6 1.0
CD2 C:HIS96 3.9 18.3 1.0
CB C:ASP210 4.0 20.8 1.0
OD1 C:ASP95 4.1 22.7 1.0
CG C:HIS91 4.2 19.4 1.0
ND1 C:HIS91 4.2 19.0 1.0
NE2 C:HIS93 4.2 23.2 1.0
ND1 C:HIS188 4.2 21.9 1.0
CG C:HIS188 4.2 21.4 1.0
CD2 C:HIS93 4.3 20.4 1.0
OD1 C:ASP210 4.4 21.9 1.0
OD2 C:ASP95 4.7 20.6 1.0
CG C:ASP95 4.8 20.9 1.0
CE1 C:HIS96 4.8 18.7 1.0
CA C:HIS93 4.9 18.2 1.0
CG C:HIS96 4.9 18.5 1.0
NE2 C:HIS279 5.0 30.7 1.0
O C:HOH502 5.0 41.2 1.0

Zinc binding site 7 out of 8 in 7bz3

Go back to Zinc Binding Sites List in 7bz3
Zinc binding site 7 out of 8 in the The Mutant Variant of Pngm-1. H257 Was Substituted For Alanine to Study Substrate Binding.


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. H257 Was Substituted For Alanine to Study Substrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:24.5
occ:1.00
 NE2 D:HIS279 1.7 26.0 1.0
O D:HOH517 2.0 19.2 1.0
NE2 D:HIS96 2.1 15.3 1.0
OD2 D:ASP95 2.3 17.7 1.0
OD2 D:ASP210 2.3 29.1 1.0
CE1 D:HIS279 2.4 30.3 1.0
CD2 D:HIS279 2.9 28.0 1.0
CD2 D:HIS96 2.9 16.7 1.0
CG D:ASP210 3.0 26.3 1.0
OD1 D:ASP210 3.0 25.9 1.0
O D:HOH642 3.2 34.3 1.0
CE1 D:HIS96 3.2 15.5 1.0
CG D:ASP95 3.2 18.4 1.0
O D:HOH695 3.4 41.1 1.0
ZN D:ZN402 3.5 20.3 1.0
OD1 D:ASP95 3.5 22.2 1.0
ND1 D:HIS279 3.6 34.9 1.0
CG D:HIS279 3.9 26.3 1.0
CG D:HIS96 4.1 16.9 1.0
CE1 D:HIS91 4.2 17.3 1.0
ND1 D:HIS96 4.2 15.9 1.0
NE2 D:HIS91 4.3 16.0 1.0
CB D:ASP210 4.5 23.3 1.0
CB D:ASP95 4.6 19.9 1.0
O D:HOH520 4.7 32.5 1.0
NE2 D:HIS188 4.8 17.5 1.0

Zinc binding site 8 out of 8 in 7bz3

Go back to Zinc Binding Sites List in 7bz3
Zinc binding site 8 out of 8 in the The Mutant Variant of Pngm-1. H257 Was Substituted For Alanine to Study Substrate Binding.


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. H257 Was Substituted For Alanine to Study Substrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:20.3
occ:1.00
 NE2 D:HIS91 2.0 16.0 1.0
ND1 D:HIS93 2.0 17.0 1.0
NE2 D:HIS188 2.1 17.5 1.0
O D:HOH517 2.1 19.2 1.0
OD2 D:ASP210 2.2 29.1 1.0
CE1 D:HIS93 2.9 20.0 1.0
CE1 D:HIS91 2.9 17.3 1.0
CD2 D:HIS188 3.0 17.3 1.0
CD2 D:HIS91 3.0 17.5 1.0
CE1 D:HIS188 3.1 18.9 1.0
CG D:HIS93 3.1 19.0 1.0
O D:HOH695 3.4 41.1 1.0
CG D:ASP210 3.4 26.3 1.0
ZN D:ZN401 3.5 24.5 1.0
CB D:HIS93 3.5 19.7 1.0
CB D:ASP210 3.9 23.3 1.0
O D:HOH642 3.9 34.3 1.0
CD2 D:HIS96 3.9 16.7 1.0
OD1 D:ASP95 4.0 22.2 1.0
NE2 D:HIS96 4.0 15.3 1.0
ND1 D:HIS91 4.1 17.9 1.0
NE2 D:HIS93 4.1 21.3 1.0
CG D:HIS91 4.1 17.9 1.0
CG D:HIS188 4.1 16.4 1.0
ND1 D:HIS188 4.1 18.1 1.0
CD2 D:HIS93 4.2 18.9 1.0
OD1 D:ASP210 4.4 25.9 1.0
OD2 D:ASP95 4.7 17.7 1.0
CG D:ASP95 4.8 18.4 1.0
CA D:HIS93 4.9 20.0 1.0
NE2 D:HIS279 5.0 26.0 1.0
CG D:HIS96 5.0 16.9 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: Tue Oct 29 17:52:45 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy