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: Mon Jul 12 16:57:23 2021

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