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Zinc in PDB 3fgg: Crystal Structure of Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus

Protein crystallography data

The structure of Crystal Structure of Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus, PDB code: 3fgg was solved by Y.Kim, B.Nocek, N.Maltseva, G.Joachimiak, J.Du, R.Jedrzejczak, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.82 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.849, 63.055, 70.374, 90.00, 115.52, 90.00
R / Rfree (%) 21.4 / 25.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus (pdb code 3fgg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus, PDB code: 3fgg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3fgg

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Zinc binding site 1 out of 8 in the Crystal Structure of Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus


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 Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn161

b:41.2
occ:1.00
OE1 A:GLU149 1.7 37.3 1.0
O3 A:GOL165 2.0 51.1 1.0
NE2 A:HIS119 2.2 34.4 1.0
O A:HOH204 2.2 19.5 1.0
CD A:GLU149 2.6 35.5 1.0
C3 A:GOL165 2.7 51.2 1.0
OE2 A:GLU149 2.9 38.6 1.0
CE1 A:HIS119 3.1 33.9 1.0
CD2 A:HIS119 3.2 27.7 1.0
O1 A:GOL165 3.4 54.4 1.0
C2 A:GOL165 3.4 50.6 1.0
CG A:GLU149 3.9 32.9 1.0
C1 A:GOL165 3.9 53.7 1.0
ND1 A:HIS119 4.2 33.3 1.0
CG A:HIS119 4.3 27.5 1.0
CD1 A:ILE132 4.5 46.9 1.0
O2 A:GOL165 4.7 51.1 1.0
CE1 A:PHE145 4.7 26.4 1.0
CZ A:PHE145 4.8 29.0 1.0
CE A:MSE152 4.9 26.0 1.0

Zinc binding site 2 out of 8 in 3fgg

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Zinc binding site 2 out of 8 in the Crystal Structure of Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus


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 Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn162

b:0.6
occ:1.00
O A:HOH170 1.9 65.8 1.0
OE2 A:GLU37 2.6 45.1 1.0
O A:HOH209 2.7 57.9 1.0
O A:HOH227 3.0 50.0 1.0
CD A:GLU37 3.5 39.5 1.0
CG A:GLU37 3.5 33.9 1.0
O A:HOH228 3.7 49.9 1.0
O A:HOH210 3.9 48.2 1.0
OD2 A:ASP36 4.1 44.4 1.0
OE1 A:GLU37 4.7 40.9 1.0
O A:HOH174 4.7 38.4 1.0
OE2 A:GLU33 4.8 49.9 1.0
CG A:GLU33 4.8 36.7 1.0

Zinc binding site 3 out of 8 in 3fgg

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Zinc binding site 3 out of 8 in the Crystal Structure of Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus


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 Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn163

b:80.7
occ:1.00
OD2 A:ASP110 2.6 35.6 1.0
O A:HOH229 2.8 44.6 1.0
OE2 A:GLU114 2.8 44.1 1.0
OE1 A:GLU114 2.9 39.6 1.0
O A:HOH223 2.9 50.1 1.0
CD A:GLU114 3.2 37.8 1.0
O A:HOH230 3.3 80.1 1.0
NZ A:LYS81 3.4 34.8 1.0
CG A:ASP110 3.7 30.5 1.0
OD1 A:ASP110 4.1 37.8 1.0
CG A:GLU114 4.7 31.6 1.0
CE A:LYS81 4.8 34.6 1.0
CB A:ASP110 5.0 27.5 1.0

Zinc binding site 4 out of 8 in 3fgg

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Zinc binding site 4 out of 8 in the Crystal Structure of Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus


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 Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn164

b:47.4
occ:1.00
NE2 A:HIS97 2.0 39.3 1.0
OD1 A:ASP156 2.2 35.7 1.0
O A:HOH213 2.5 46.5 1.0
OD2 A:ASP156 2.6 35.8 1.0
CG A:ASP156 2.7 33.4 1.0
CE1 A:HIS97 2.9 43.7 1.0
CD2 A:HIS97 3.1 41.4 1.0
O A:HOH198 3.8 36.1 1.0
NH1 A:ARG160 4.0 57.5 1.0
ND1 A:HIS97 4.1 44.9 1.0
CG A:HIS97 4.2 41.1 1.0
CB A:ASP156 4.2 32.5 1.0
CD A:ARG160 4.5 54.7 1.0
O A:ASP156 4.5 34.0 1.0
CA A:ASP156 4.9 31.9 1.0

Zinc binding site 5 out of 8 in 3fgg

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Zinc binding site 5 out of 8 in the Crystal Structure of Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus


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 Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn161

b:44.0
occ:1.00
OE1 B:GLU149 1.7 36.7 1.0
NE2 B:HIS119 2.1 35.5 1.0
O B:HOH194 2.1 27.5 1.0
O1 B:GOL165 2.4 59.9 1.0
CD B:GLU149 2.7 35.1 1.0
O3 B:GOL165 2.9 55.0 1.0
CE1 B:HIS119 3.0 34.7 1.0
OE2 B:GLU149 3.1 38.6 1.0
CD2 B:HIS119 3.2 29.4 1.0
C1 B:GOL165 3.7 58.9 1.0
CG B:GLU149 4.0 31.9 1.0
C3 B:GOL165 4.0 56.0 1.0
ND1 B:HIS119 4.1 33.5 1.0
CG B:HIS119 4.2 28.2 1.0
C2 B:GOL165 4.3 57.8 1.0
CD1 B:ILE132 4.4 45.4 1.0
CZ B:PHE145 4.6 26.2 1.0
CE1 B:PHE145 4.8 27.1 1.0
CE B:MSE152 4.8 27.2 1.0
O A:HOH188 4.9 41.4 1.0

Zinc binding site 6 out of 8 in 3fgg

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Zinc binding site 6 out of 8 in the Crystal Structure of Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus


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 Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn162

b:43.6
occ:1.00
OD1 B:ASP156 2.0 29.1 1.0
NE2 B:HIS97 2.1 38.5 1.0
O B:HOH199 2.2 38.6 1.0
CG B:ASP156 2.9 29.0 1.0
CE1 B:HIS97 3.0 40.7 1.0
OD2 B:ASP156 3.1 35.2 1.0
CD2 B:HIS97 3.2 37.4 1.0
ND1 B:HIS97 4.1 41.0 1.0
O B:ARG160 4.2 44.9 0.5
CG B:HIS97 4.2 37.6 1.0
C B:ARG160 4.3 44.9 0.5
CB B:ASP156 4.3 29.8 1.0
O B:ASP156 4.7 32.0 1.0
O B:HOH208 4.9 30.5 1.0
CA B:ASP156 4.9 29.5 1.0
O B:HOH214 4.9 42.1 1.0
C B:ARG160 5.0 45.0 0.5

Zinc binding site 7 out of 8 in 3fgg

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Zinc binding site 7 out of 8 in the Crystal Structure of Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus


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 Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn163

b:83.8
occ:1.00
OD1 B:ASP110 2.6 37.0 1.0
O B:HOH215 2.6 44.9 1.0
O B:HOH216 2.7 52.6 1.0
O B:HOH213 2.8 42.1 1.0
OE1 B:GLU114 2.9 41.5 1.0
OE2 B:GLU114 3.2 44.1 1.0
O B:HOH200 3.4 54.7 1.0
CD B:GLU114 3.4 38.6 1.0
NZ B:LYS81 3.4 32.8 1.0
CG B:ASP110 3.5 30.6 1.0
O B:HOH195 3.5 42.8 1.0
OD2 B:ASP110 3.7 33.2 1.0
O B:HOH217 4.3 65.2 1.0
CE B:LYS81 4.7 33.2 1.0
CB B:ASP110 4.8 26.4 1.0
CG B:GLU114 4.9 30.7 1.0

Zinc binding site 8 out of 8 in 3fgg

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Zinc binding site 8 out of 8 in the Crystal Structure of Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus


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 Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn164

b:0.3
occ:1.00
OE2 B:GLU37 2.7 42.8 1.0
O B:HOH197 2.8 52.7 1.0
CD B:GLU37 3.5 39.5 1.0
CG B:GLU37 3.6 32.8 1.0
OD2 B:ASP36 4.4 41.1 1.0
CG B:GLU33 4.6 36.1 1.0
O B:HOH220 4.7 40.8 1.0
OE1 B:GLU37 4.7 42.3 1.0

Reference:

Y.Kim, B.Nocek, N.Maltseva, G.Joachimiak, J.Du, R.Jedrzejczak, A.Joachimiak. Crystal Structure of Putative Ecf-Type Sigma Factor Negative Effector From Bacillus Cereus To Be Published.
Page generated: Sat Sep 26 06:27:27 2020
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