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Zinc in PDB 1xtl: Crystal Structure of P104H Mutant of Sod-Like Protein From Bacillus Subtilis.

Protein crystallography data

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

Resolution Low / High (Å) 38.92 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.147, 56.586, 59.118, 78.24, 89.91, 85.47
R / Rfree (%) 23.2 / 29.9

Other elements in 1xtl:

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

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of P104H Mutant of Sod-Like Protein From Bacillus Subtilis. (pdb code 1xtl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of P104H Mutant of Sod-Like Protein From Bacillus Subtilis., PDB code: 1xtl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 1xtl

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Zinc binding site 1 out of 10 in the Crystal Structure of P104H Mutant of 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 P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1172

b:29.3
occ:1.00
ND1 B:HIS121 2.0 20.2 1.0
OD1 B:ASP124 2.1 22.3 1.0
ND1 B:HIS104 2.2 20.1 1.0
ND1 B:HIS112 2.3 24.2 1.0
CE1 B:HIS121 2.9 17.9 1.0
CG B:ASP124 3.0 20.3 1.0
CG B:HIS104 3.1 13.3 1.0
CG B:HIS121 3.1 19.9 1.0
OD2 B:ASP124 3.2 21.6 1.0
CE1 B:HIS112 3.2 21.4 1.0
CE1 B:HIS104 3.2 20.2 1.0
CB B:HIS104 3.3 16.2 1.0
CG B:HIS112 3.4 22.0 1.0
CB B:HIS121 3.4 21.4 1.0
CB B:HIS112 3.7 20.9 1.0
O B:PRO176 3.8 20.6 1.0
CA B:HIS112 4.0 20.9 1.0
NE2 B:HIS121 4.1 15.5 1.0
CD2 B:HIS121 4.2 10.8 1.0
CD2 B:HIS104 4.2 17.5 1.0
NE2 B:HIS104 4.3 7.5 1.0
NE2 B:HIS112 4.4 20.9 1.0
CB B:ASP124 4.4 22.9 1.0
CD2 B:HIS112 4.4 24.1 1.0
ND1 B:HIS86 4.6 21.1 1.0
O B:HOH1339 4.7 26.0 1.0
CA B:HIS121 4.8 24.5 1.0
CA B:ASP124 4.8 22.5 1.0
N B:ASP124 4.9 23.3 1.0
N B:GLY113 4.9 21.5 1.0
N B:HIS121 4.9 25.3 1.0
N B:HIS112 4.9 22.6 1.0
CE1 B:HIS86 4.9 22.2 1.0
CA B:HIS104 4.9 17.9 1.0
C B:PRO176 5.0 20.4 1.0
C B:HIS112 5.0 21.8 1.0

Zinc binding site 2 out of 10 in 1xtl

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Zinc binding site 2 out of 10 in the Crystal Structure of P104H Mutant of 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 P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1326

b:26.4
occ:1.00
OD1 B:ASP137 2.0 28.0 1.0
NE2 B:HIS71 2.3 27.7 1.0
CG B:ASP137 2.8 23.3 1.0
OD2 B:ASP137 2.9 20.5 1.0
CE1 B:HIS71 3.2 18.0 1.0
CD2 B:HIS71 3.3 26.3 1.0
CB B:SER73 4.2 22.8 1.0
OG B:SER73 4.2 23.0 1.0
CB B:ASP137 4.2 21.0 1.0
ND1 B:HIS71 4.3 21.6 1.0
CG B:HIS71 4.4 24.5 1.0
O B:ASP137 4.6 22.7 1.0
C B:ASP137 4.6 21.8 1.0
CA B:ASP137 4.7 23.3 1.0

Zinc binding site 3 out of 10 in 1xtl

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Zinc binding site 3 out of 10 in the Crystal Structure of P104H Mutant of 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 P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1329

b:39.1
occ:1.00
O B:GLY160 2.4 21.7 1.0
O B:HOH1378 2.4 26.3 1.0
OD2 B:ASP157 2.4 19.7 1.0
O B:HOH1396 2.5 15.8 1.0
OD1 B:ASP157 2.5 26.0 1.0
O B:GLU89 2.6 19.4 1.0
CG B:ASP157 2.8 26.7 1.0
CB B:ASP159 2.9 28.5 1.0
C B:GLY160 3.6 23.1 1.0
C B:GLU89 3.7 18.4 1.0
CG B:ASP159 3.8 34.3 1.0
N B:GLY160 3.8 26.6 1.0
C B:ASP159 3.9 27.1 1.0
OD1 B:ASP159 4.0 36.8 1.0
CA B:ASP159 4.0 28.5 1.0
OG B:SER161 4.4 20.5 1.0
CB B:ASP157 4.4 27.0 1.0
CA B:GLY160 4.4 23.8 1.0
CA B:GLU89 4.4 17.9 1.0
O B:ASP159 4.5 25.3 1.0
O B:HOH1405 4.5 24.2 1.0
CA B:LYS90 4.5 19.5 1.0
N B:LYS90 4.6 16.3 1.0
N B:SER161 4.6 21.7 1.0
O B:HOH1342 4.7 28.2 1.0
N B:ASP159 4.7 27.4 1.0
CB B:GLU89 4.9 19.8 1.0
OD2 B:ASP159 4.9 43.5 1.0
CA B:SER161 4.9 19.8 1.0
O B:ILE155 5.0 25.8 1.0

Zinc binding site 4 out of 10 in 1xtl

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Zinc binding site 4 out of 10 in the Crystal Structure of P104H Mutant of 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 P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1174

b:25.2
occ:1.00
ND1 A:HIS104 1.8 20.9 1.0
OD1 A:ASP124 2.0 18.8 1.0
ND1 A:HIS121 2.1 19.8 1.0
ND1 A:HIS112 2.3 14.4 1.0
CE1 A:HIS104 2.7 17.1 1.0
CG A:HIS104 2.9 19.5 1.0
CE1 A:HIS121 3.0 21.8 1.0
CG A:ASP124 3.0 23.1 1.0
CG A:HIS121 3.2 24.8 1.0
CE1 A:HIS112 3.2 12.6 1.0
OD2 A:ASP124 3.4 25.9 1.0
CB A:HIS104 3.4 20.8 1.0
CG A:HIS112 3.4 16.7 1.0
CB A:HIS121 3.6 26.2 1.0
CB A:HIS112 3.8 14.0 1.0
O A:PRO176 3.8 24.0 1.0
NE2 A:HIS104 3.8 11.5 1.0
CD2 A:HIS104 3.9 16.5 1.0
CA A:HIS112 4.1 16.2 1.0
NE2 A:HIS121 4.1 20.9 1.0
CD2 A:HIS121 4.2 18.0 1.0
NE2 A:HIS112 4.4 13.3 1.0
CB A:ASP124 4.4 24.5 1.0
CD2 A:HIS112 4.5 16.8 1.0
CD2 A:HIS86 4.7 22.0 1.0
CA A:ASP124 4.8 22.9 1.0
CA A:SER177 4.8 24.6 1.0
N A:ASP124 4.8 23.6 1.0
C A:PRO176 4.9 24.1 1.0
CA A:HIS121 4.9 25.9 1.0
CA A:HIS104 5.0 21.0 1.0
O A:HOH1348 5.0 21.7 1.0
N A:HIS112 5.0 17.8 1.0

Zinc binding site 5 out of 10 in 1xtl

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Zinc binding site 5 out of 10 in the Crystal Structure of P104H Mutant of 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 P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1327

b:26.9
occ:1.00
OD1 A:ASP137 2.1 29.8 1.0
NE2 A:HIS71 2.2 29.5 1.0
OD2 A:ASP137 2.6 24.5 1.0
CG A:ASP137 2.7 25.8 1.0
CE1 A:HIS71 3.1 24.1 1.0
CD2 A:HIS71 3.1 22.9 1.0
CB A:ASP137 4.1 21.6 1.0
ND1 A:HIS71 4.2 21.1 1.0
OG A:SER73 4.2 19.2 1.0
CG A:HIS71 4.2 22.5 1.0
O A:ASP137 4.4 20.7 1.0
C A:ASP137 4.5 21.2 1.0
CB A:SER73 4.6 26.2 1.0
CA A:ASP137 4.7 22.9 1.0
N A:VAL138 4.8 20.5 1.0

Zinc binding site 6 out of 10 in 1xtl

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Zinc binding site 6 out of 10 in the Crystal Structure of P104H Mutant of 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 6 of Crystal Structure of P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1331

b:41.1
occ:1.00
OD1 A:ASP159 2.3 17.7 1.0
OD1 A:ASP157 2.4 27.7 1.0
OD2 A:ASP157 2.5 25.2 1.0
O A:GLY160 2.5 22.5 1.0
O A:GLU89 2.8 18.8 1.0
CG A:ASP157 2.8 31.7 1.0
CG A:ASP159 3.6 25.1 1.0
C A:GLY160 3.6 21.3 1.0
C A:GLU89 3.8 19.0 1.0
N A:GLY160 3.9 22.5 1.0
OG A:SER161 4.2 16.2 1.0
OD2 A:ASP159 4.2 26.7 1.0
C A:ASP159 4.2 23.8 1.0
CB A:ASP157 4.3 31.7 1.0
CA A:GLY160 4.3 21.5 1.0
O A:HOH1359 4.6 23.7 1.0
CA A:ASP159 4.6 25.2 1.0
CA A:GLU89 4.6 20.4 1.0
O A:HOH1392 4.6 35.6 1.0
N A:SER161 4.7 19.5 1.0
CB A:ASP159 4.7 26.0 1.0
N A:ASP159 4.7 27.3 1.0
N A:LYS90 4.7 18.3 1.0
CA A:LYS90 4.7 19.6 1.0
O A:ASP159 4.8 25.5 1.0
CA A:SER161 4.9 17.5 1.0
CB A:GLU89 5.0 22.3 1.0

Zinc binding site 7 out of 10 in 1xtl

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Zinc binding site 7 out of 10 in the Crystal Structure of P104H Mutant of 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 7 of Crystal Structure of P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1176

b:23.7
occ:1.00
ND1 C:HIS112 2.0 11.6 1.0
ND1 C:HIS104 2.1 6.9 1.0
OD1 C:ASP124 2.2 25.5 1.0
ND1 C:HIS121 2.3 23.4 1.0
CE1 C:HIS112 2.7 9.6 1.0
CG C:HIS104 3.0 13.7 1.0
CE1 C:HIS121 3.1 15.7 1.0
CG C:ASP124 3.1 24.0 1.0
CE1 C:HIS104 3.1 11.2 1.0
CG C:HIS112 3.2 19.5 1.0
CB C:HIS104 3.2 18.8 1.0
OD2 C:ASP124 3.4 28.7 1.0
CG C:HIS121 3.5 22.7 1.0
O C:PRO176 3.6 21.4 1.0
CB C:HIS112 3.7 21.4 1.0
CB C:HIS121 3.9 20.9 1.0
NE2 C:HIS112 3.9 14.4 1.0
CA C:HIS112 4.1 23.2 1.0
CD2 C:HIS104 4.2 15.2 1.0
CD2 C:HIS112 4.2 16.9 1.0
NE2 C:HIS104 4.2 11.6 1.0
NE2 C:HIS121 4.3 19.5 1.0
CD2 C:HIS86 4.3 18.1 1.0
CB C:ASP124 4.5 23.5 1.0
CD2 C:HIS121 4.5 18.9 1.0
O C:HOH1343 4.7 25.1 1.0
C C:PRO176 4.7 23.8 1.0
NE2 C:HIS86 4.8 19.7 1.0
CA C:SER177 4.8 26.8 1.0
CA C:HIS104 4.8 18.4 1.0
CA C:ASP124 4.8 22.7 1.0
N C:HIS121 4.9 23.0 1.0
N C:ASP124 5.0 22.6 1.0

Zinc binding site 8 out of 10 in 1xtl

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Zinc binding site 8 out of 10 in the Crystal Structure of P104H Mutant of 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 8 of Crystal Structure of P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1328

b:39.7
occ:1.00
O C:GLY160 2.4 24.0 1.0
OD1 C:ASP157 2.5 29.0 1.0
OD2 C:ASP157 2.6 34.5 1.0
O C:GLU89 2.6 26.1 1.0
CG C:ASP157 2.9 29.5 1.0
CB C:ASP159 3.0 29.9 1.0
C C:GLY160 3.5 22.7 1.0
C C:GLU89 3.6 23.6 1.0
OD1 C:ASP159 3.7 30.6 1.0
CG C:ASP159 3.8 32.2 1.0
N C:GLY160 3.8 25.0 1.0
C C:ASP159 4.0 28.2 1.0
CA C:ASP159 4.1 30.0 1.0
CA C:GLY160 4.2 23.4 1.0
CB C:ASP157 4.4 31.0 1.0
OG C:SER161 4.4 26.5 1.0
CA C:GLU89 4.5 25.3 1.0
N C:ASP159 4.5 30.1 1.0
N C:LYS90 4.5 23.8 1.0
N C:SER161 4.6 23.0 1.0
O C:ASP159 4.6 27.0 1.0
CA C:LYS90 4.7 22.8 1.0
CA C:SER161 4.9 22.1 1.0
O C:ILE155 4.9 27.9 1.0
CB C:GLU89 4.9 26.0 1.0
OD2 C:ASP159 4.9 40.5 1.0

Zinc binding site 9 out of 10 in 1xtl

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Zinc binding site 9 out of 10 in the Crystal Structure of P104H Mutant of 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 9 of Crystal Structure of P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1178

b:22.3
occ:1.00
ND1 D:HIS112 1.9 12.9 1.0
ND1 D:HIS121 2.0 20.0 1.0
OD1 D:ASP124 2.1 17.9 1.0
ND1 D:HIS104 2.3 2.0 1.0
CE1 D:HIS112 2.8 16.0 1.0
CE1 D:HIS121 2.8 17.6 1.0
CG D:ASP124 3.0 22.7 1.0
CG D:HIS104 3.0 4.3 1.0
CG D:HIS121 3.1 26.9 1.0
CB D:HIS104 3.1 17.9 1.0
CG D:HIS112 3.1 21.2 1.0
OD2 D:ASP124 3.2 30.4 1.0
CE1 D:HIS104 3.4 20.6 1.0
CB D:HIS121 3.5 23.4 1.0
CB D:HIS112 3.6 24.6 1.0
O D:PRO176 3.7 21.4 1.0
NE2 D:HIS112 3.9 17.3 1.0
NE2 D:HIS121 4.0 22.6 1.0
CA D:HIS112 4.1 26.1 1.0
CD2 D:HIS112 4.1 18.4 1.0
CD2 D:HIS121 4.1 22.4 1.0
CD2 D:HIS104 4.3 14.9 1.0
CB D:ASP124 4.4 24.1 1.0
NE2 D:HIS104 4.4 2.0 1.0
O D:HOH1338 4.6 36.1 1.0
CA D:HIS104 4.7 17.0 1.0
CA D:HIS121 4.7 24.2 1.0
C D:PRO176 4.8 23.7 1.0
CA D:ASP124 4.8 24.3 1.0
N D:HIS121 4.8 27.5 1.0
CA D:SER177 4.9 27.1 1.0
N D:GLY113 5.0 28.4 1.0
N D:ASP124 5.0 23.0 1.0
CD2 D:HIS86 5.0 26.5 1.0
N D:HIS112 5.0 27.8 1.0

Zinc binding site 10 out of 10 in 1xtl

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Zinc binding site 10 out of 10 in the Crystal Structure of P104H Mutant of 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 10 of Crystal Structure of P104H Mutant of Sod-Like Protein From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1330

b:40.3
occ:1.00
OD1 D:ASP157 2.4 21.0 1.0
O D:GLU89 2.5 22.6 1.0
O D:GLY160 2.5 22.9 1.0
OD2 D:ASP157 2.6 26.2 1.0
O D:HOH1392 2.7 17.9 1.0
CG D:ASP157 2.9 25.0 1.0
CB D:ASP159 3.0 27.5 1.0
C D:GLY160 3.5 22.1 1.0
N D:GLY160 3.5 21.9 1.0
C D:GLU89 3.6 23.1 1.0
CG D:ASP159 3.8 28.4 1.0
OD1 D:ASP159 3.8 28.4 1.0
C D:ASP159 3.9 24.4 1.0
CA D:ASP159 4.0 26.6 1.0
CA D:GLY160 4.1 21.3 1.0
CB D:ASP157 4.4 27.1 1.0
N D:LYS90 4.4 22.0 1.0
CA D:GLU89 4.5 22.1 1.0
N D:ASP159 4.5 27.4 1.0
CA D:LYS90 4.5 24.0 1.0
N D:SER161 4.5 23.7 1.0
OG D:SER161 4.6 22.2 1.0
O D:ASP159 4.6 24.2 1.0
OD2 D:ASP159 4.9 38.8 1.0
CB D:GLU89 4.9 22.9 1.0
CA D:SER161 5.0 22.6 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

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