Atomistry » Zinc » PDB 1xm6-1xug » 1xtm
Atomistry »
  Zinc »
    PDB 1xm6-1xug »
      1xtm »

Zinc in PDB 1xtm: Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.

Protein crystallography data

The structure of Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis., PDB code: 1xtm was solved by V.Calderone, S.Mangani, L.Banci, M.Benvenuti, I.Bertini, A.Fantoni, M.S.Viezzoli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.60 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 52.462, 104.350, 58.756, 90.00, 90.00, 90.00
R / Rfree (%) 25.3 / 26.6

Other elements in 1xtm:

The structure of Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. (pdb code 1xtm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis., PDB code: 1xtm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 1xtm

Go back to Zinc Binding Sites List in 1xtm
Zinc binding site 1 out of 5 in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:20.3
occ:1.00
OD2 B:ASP124 2.0 8.8 1.0
ND1 B:HIS104 2.0 13.3 1.0
ND1 B:HIS121 2.0 17.5 1.0
ND1 B:HIS112 2.1 12.1 1.0
CE1 B:HIS104 2.8 19.3 1.0
CG B:ASP124 2.8 14.5 1.0
CE1 B:HIS112 2.9 10.6 1.0
CE1 B:HIS121 2.9 13.4 1.0
OD1 B:ASP124 2.9 15.9 1.0
CG B:HIS121 3.1 13.8 1.0
CG B:HIS104 3.1 15.5 1.0
CG B:HIS112 3.2 15.6 1.0
CB B:HIS121 3.5 12.7 1.0
CB B:HIS104 3.6 14.8 1.0
CB B:HIS112 3.6 17.7 1.0
O B:PRO176 3.8 25.9 1.0
NE2 B:HIS104 4.0 18.5 1.0
CA B:HIS112 4.0 17.3 1.0
NE2 B:HIS121 4.1 17.5 1.0
NE2 B:HIS112 4.1 12.0 1.0
CD2 B:HIS104 4.2 15.6 1.0
CD2 B:HIS121 4.2 16.8 1.0
CD2 B:HIS112 4.2 15.4 1.0
CB B:ASP124 4.3 11.4 1.0
N B:HIS121 4.7 13.7 1.0
N B:GLY113 4.7 16.7 1.0
CA B:HIS121 4.7 12.9 1.0
CA B:ASP124 4.8 11.4 1.0
C B:HIS112 4.9 16.3 1.0
C B:PRO176 4.9 26.7 1.0
O B:HOH567 4.9 34.9 1.0
CD2 B:HIS86 4.9 16.1 1.0
N B:ASP124 5.0 10.5 1.0

Zinc binding site 2 out of 5 in 1xtm

Go back to Zinc Binding Sites List in 1xtm
Zinc binding site 2 out of 5 in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:21.4
occ:1.00
OD1 B:ASP137 1.9 13.2 1.0
NE2 B:HIS71 2.2 19.3 1.0
CG B:ASP137 2.8 14.0 1.0
OD2 B:ASP137 2.9 18.5 1.0
CE1 B:HIS71 3.0 19.3 1.0
CD2 B:HIS71 3.2 16.6 1.0
ND1 B:HIS71 4.2 18.0 1.0
CB B:ASP137 4.2 16.6 1.0
CB B:SER73 4.2 14.7 1.0
OG B:SER73 4.3 16.9 1.0
CG B:HIS71 4.3 16.9 1.0
C B:ASP137 4.6 16.3 1.0
CA B:ASP137 4.7 15.8 1.0
O B:ASP137 4.8 15.1 1.0
N B:VAL138 4.8 16.5 1.0

Zinc binding site 3 out of 5 in 1xtm

Go back to Zinc Binding Sites List in 1xtm
Zinc binding site 3 out of 5 in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn505

b:26.9
occ:0.30
O B:HOH553 2.0 28.8 1.0
O B:HOH642 2.0 39.8 1.0
OD2 B:ASP144 2.2 15.0 1.0
NE2 B:HIS120 2.3 24.5 1.0
CE1 B:HIS120 3.0 23.6 1.0
CG B:ASP144 3.1 15.0 1.0
CD2 B:HIS120 3.4 21.2 1.0
OD1 B:ASP144 3.7 15.0 1.0
CB B:ASP144 4.0 15.0 1.0
ND1 B:HIS120 4.2 21.7 1.0
O B:HOH523 4.3 20.2 1.0
O B:HOH530 4.3 18.1 1.0
CG B:HIS120 4.4 18.7 1.0
CG B:PRO143 4.6 19.3 1.0
N B:ASP144 5.0 15.0 1.0

Zinc binding site 4 out of 5 in 1xtm

Go back to Zinc Binding Sites List in 1xtm
Zinc binding site 4 out of 5 in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn506

b:22.0
occ:0.50
OD2 B:ASP157 2.3 27.2 1.0
OD1 B:ASP157 2.5 26.2 1.0
O B:HOH628 2.5 24.9 1.0
O B:GLY160 2.5 16.3 1.0
O B:GLU89 2.5 17.1 1.0
CG B:ASP157 2.8 26.3 1.0
CB B:ASP159 3.1 15.0 1.0
O B:HOH609 3.4 28.2 1.0
C B:GLY160 3.5 15.4 1.0
C B:GLU89 3.7 15.6 1.0
N B:GLY160 3.9 18.8 1.0
CA B:ASP159 4.1 15.0 1.0
C B:ASP159 4.1 15.0 1.0
OG B:SER161 4.1 16.2 1.0
CG B:ASP159 4.2 15.0 1.0
CA B:GLY160 4.2 16.1 1.0
O B:HOH631 4.3 41.5 1.0
CB B:ASP157 4.3 24.0 1.0
OD2 B:ASP159 4.3 15.0 1.0
CA B:GLU89 4.5 15.4 1.0
N B:ASP159 4.5 15.0 1.0
N B:LYS90 4.6 16.2 1.0
N B:SER161 4.6 13.2 1.0
O B:ASP159 4.6 20.3 1.0
CA B:LYS90 4.7 16.6 1.0
CA B:SER161 4.8 12.9 1.0
O B:ILE155 4.9 17.3 1.0
O B:HOH613 4.9 28.8 1.0

Zinc binding site 5 out of 5 in 1xtm

Go back to Zinc Binding Sites List in 1xtm
Zinc binding site 5 out of 5 in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:33.0
occ:0.80
ND1 A:HIS121 1.9 36.5 1.0
OD2 A:ASP124 2.0 27.5 1.0
ND1 A:HIS104 2.1 32.1 1.0
ND1 A:HIS112 2.1 32.9 1.0
CE1 A:HIS121 2.7 35.9 1.0
CG A:ASP124 2.9 28.1 1.0
CE1 A:HIS104 2.9 31.6 1.0
CG A:HIS121 3.0 35.5 1.0
OD1 A:ASP124 3.1 29.9 1.0
CE1 A:HIS112 3.1 32.8 1.0
CG A:HIS112 3.2 35.0 1.0
CG A:HIS104 3.2 34.8 1.0
CB A:HIS112 3.5 35.0 1.0
CB A:HIS121 3.5 35.5 1.0
CB A:HIS104 3.6 38.1 1.0
O A:PRO176 3.8 31.9 1.0
NE2 A:HIS121 3.9 35.3 1.0
CA A:HIS112 4.0 35.1 1.0
CD2 A:HIS121 4.1 36.0 1.0
NE2 A:HIS104 4.1 33.5 1.0
NE2 A:HIS112 4.2 32.5 1.0
CD2 A:HIS104 4.2 33.6 1.0
CD2 A:HIS86 4.3 27.9 1.0
CD2 A:HIS112 4.3 33.0 1.0
CB A:ASP124 4.4 28.2 1.0
N A:GLY113 4.8 33.9 1.0
CA A:HIS121 4.8 35.6 1.0
NE2 A:HIS86 4.8 28.0 1.0
N A:HIS121 4.8 36.2 1.0
CA A:ASP124 4.9 27.8 1.0
CG A:HIS86 4.9 27.1 1.0
C A:HIS112 4.9 34.7 1.0
C A:PRO176 4.9 31.6 1.0
N A:HIS112 5.0 35.9 1.0

Reference:

L.Banci, M.Benvenuti, I.Bertini, D.E.Cabelli, V.Calderone, A.Fantoni, S.Mangani, M.Migliardi, M.S.Viezzoli. From An Inactive Prokaryotic Sod Homologue to An Active Protein Through Site-Directed Mutagenesis. J.Am.Chem.Soc. V. 127 13287 2005.
ISSN: ISSN 0002-7863
PubMed: 16173759
DOI: 10.1021/JA052790O
Page generated: Wed Dec 16 03:13:10 2020

Last articles

Ca in 5ZZ0
Ca in 6AG0
Ca in 6AGI
Ca in 6A56
Ca in 6ADU
Ca in 6AH4
Ca in 6AGK
Ca in 6A8X
Ca in 6AG5
Ca in 6AG4
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy