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Zinc in PDB 3k2g: Crystal Structure of A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides

Protein crystallography data

The structure of Crystal Structure of A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides, PDB code: 3k2g was solved by D.Kumaran, S.K.Burley, S.Swaminathan, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.79 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 179.735, 47.414, 188.934, 90.00, 108.34, 90.00
R / Rfree (%) 20.4 / 22.5

Other elements in 3k2g:

The structure of Crystal Structure of A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides (pdb code 3k2g). 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 A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides, PDB code: 3k2g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3k2g

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Zinc binding site 1 out of 8 in the Crystal Structure of A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides


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 A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:21.6
occ:1.00
O A:HOH872 2.1 13.7 1.0
OE2 A:GLU175 2.1 10.1 1.0
NE2 A:HIS32 2.1 11.0 1.0
NE2 A:HIS34 2.2 14.2 1.0
OD1 A:ASP302 2.3 9.8 1.0
CD2 A:HIS34 3.1 12.3 1.0
CE1 A:HIS32 3.1 14.6 1.0
CD2 A:HIS32 3.2 15.0 1.0
CG A:ASP302 3.2 15.4 1.0
CD A:GLU175 3.2 17.1 1.0
CE1 A:HIS34 3.2 15.0 1.0
O A:HOH610 3.2 26.3 1.0
OD2 A:ASP302 3.4 11.8 1.0
OE1 A:GLU175 3.6 12.2 1.0
ZN A:ZN401 3.6 28.2 1.0
ND1 A:HIS32 4.2 11.9 1.0
CG A:HIS34 4.3 12.3 1.0
ND1 A:HIS34 4.3 12.1 1.0
CG A:HIS32 4.3 13.0 1.0
CE1 A:HIS236 4.3 18.3 1.0
CB A:ASP302 4.5 10.6 1.0
CG A:GLU175 4.5 16.4 1.0
CG A:PRO104 4.6 13.6 1.0
NE2 A:HIS236 4.6 17.0 1.0
O A:HOH372 4.6 26.9 1.0
O A:HOH436 4.6 18.1 1.0
OH A:TYR134 4.8 24.0 1.0
CA A:ASP302 4.9 10.8 1.0

Zinc binding site 2 out of 8 in 3k2g

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Zinc binding site 2 out of 8 in the Crystal Structure of A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides


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 A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:28.2
occ:1.00
O A:HOH872 2.2 13.7 1.0
OE1 A:GLU175 2.3 12.2 1.0
ND1 A:HIS207 2.4 14.7 1.0
NE2 A:HIS236 2.4 17.0 1.0
O A:HOH372 2.4 26.9 1.0
OH A:TYR134 2.5 24.0 1.0
CD A:GLU175 3.0 17.1 1.0
CE1 A:HIS236 3.2 18.3 1.0
CE1 A:HIS207 3.2 15.9 1.0
OE2 A:GLU175 3.3 10.1 1.0
CG A:HIS207 3.4 16.5 1.0
CD2 A:HIS236 3.4 19.6 1.0
CZ A:TYR134 3.6 25.9 1.0
ZN A:ZN400 3.6 21.6 1.0
CE1 A:TYR134 3.7 24.3 1.0
CB A:HIS207 3.8 14.1 1.0
O A:HOH610 4.1 26.3 1.0
CG A:GLU175 4.3 16.4 1.0
ND1 A:HIS236 4.4 16.6 1.0
NE2 A:HIS207 4.4 14.7 1.0
CE1 A:HIS32 4.4 14.6 1.0
OD2 A:ASP302 4.5 11.8 1.0
NE2 A:HIS32 4.5 11.0 1.0
CD2 A:HIS207 4.5 15.5 1.0
CG A:HIS236 4.5 18.3 1.0
CA A:HIS207 4.6 15.3 1.0
CE2 A:TYR134 4.8 24.6 1.0
O3 A:DTV402 4.8 37.2 1.0

Zinc binding site 3 out of 8 in 3k2g

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Zinc binding site 3 out of 8 in the Crystal Structure of A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides


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 A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:22.2
occ:1.00
O B:HOH363 2.0 19.4 1.0
NE2 B:HIS34 2.2 17.7 1.0
NE2 B:HIS32 2.2 15.6 1.0
OE2 B:GLU175 2.3 13.8 1.0
OD1 B:ASP302 2.3 16.3 1.0
O B:HOH870 2.9 26.0 1.0
CD2 B:HIS34 3.1 17.4 1.0
CE1 B:HIS34 3.2 19.6 1.0
CG B:ASP302 3.2 16.5 1.0
CD2 B:HIS32 3.2 15.3 1.0
CE1 B:HIS32 3.2 17.9 1.0
CD B:GLU175 3.3 21.0 1.0
OD2 B:ASP302 3.5 15.7 1.0
OE1 B:GLU175 3.6 14.8 1.0
ZN B:ZN401 3.6 33.5 1.0
CE1 B:HIS236 4.2 20.2 1.0
ND1 B:HIS34 4.3 16.9 1.0
CG B:HIS34 4.3 19.2 1.0
ND1 B:HIS32 4.3 14.8 1.0
CG B:HIS32 4.4 15.3 1.0
CB B:ASP302 4.5 13.8 1.0
NE2 B:HIS236 4.5 15.9 1.0
O B:HOH772 4.5 28.2 1.0
CG B:PRO104 4.6 17.0 1.0
CG B:GLU175 4.6 21.0 1.0
O B:HOH394 4.7 20.6 1.0
OH B:TYR134 4.8 28.0 1.0
CA B:ASP302 4.9 14.1 1.0
O3 B:DTV402 4.9 41.1 1.0

Zinc binding site 4 out of 8 in 3k2g

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Zinc binding site 4 out of 8 in the Crystal Structure of A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides


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 A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:33.5
occ:1.00
O B:HOH363 2.1 19.4 1.0
ND1 B:HIS207 2.1 19.8 1.0
NE2 B:HIS236 2.3 15.9 1.0
OE1 B:GLU175 2.4 14.8 1.0
O B:HOH772 2.4 28.2 1.0
OH B:TYR134 2.7 28.0 1.0
CE1 B:HIS207 2.9 22.9 1.0
CE1 B:HIS236 3.2 20.2 1.0
CD B:GLU175 3.2 21.0 1.0
CG B:HIS207 3.3 19.2 1.0
CD2 B:HIS236 3.3 19.6 1.0
OE2 B:GLU175 3.6 13.8 1.0
ZN B:ZN400 3.6 22.2 1.0
CZ B:TYR134 3.7 27.9 1.0
CB B:HIS207 3.7 20.1 1.0
CE1 B:TYR134 3.8 28.1 1.0
O B:HOH870 4.0 26.0 1.0
NE2 B:HIS207 4.1 22.5 1.0
CD2 B:HIS207 4.3 22.1 1.0
ND1 B:HIS236 4.3 18.0 1.0
O3 B:DTV402 4.4 41.1 1.0
CG B:GLU175 4.4 21.0 1.0
CG B:HIS236 4.4 18.5 1.0
CE1 B:HIS32 4.6 17.9 1.0
NE2 B:HIS32 4.6 15.6 1.0
CA B:HIS207 4.6 17.7 1.0
OD2 B:ASP302 4.6 15.7 1.0
C1 B:DTV402 4.9 42.2 1.0
CE2 B:TYR134 5.0 28.3 1.0

Zinc binding site 5 out of 8 in 3k2g

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Zinc binding site 5 out of 8 in the Crystal Structure of A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides


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 A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn400

b:15.5
occ:1.00
O C:HOH364 1.9 13.1 1.0
NE2 C:HIS34 2.1 15.1 1.0
NE2 C:HIS32 2.2 10.1 1.0
OE2 C:GLU175 2.3 13.0 1.0
OD1 C:ASP302 2.3 11.0 1.0
O C:HOH869 3.1 29.8 1.0
CD2 C:HIS34 3.1 12.4 1.0
CE1 C:HIS34 3.1 16.0 1.0
CE1 C:HIS32 3.2 13.1 1.0
CD2 C:HIS32 3.2 10.8 1.0
CG C:ASP302 3.3 14.2 1.0
CD C:GLU175 3.3 17.9 1.0
OE1 C:GLU175 3.5 11.7 1.0
OD2 C:ASP302 3.5 15.7 1.0
ZN C:ZN401 3.5 28.9 1.0
ND1 C:HIS34 4.2 13.8 1.0
CG C:HIS34 4.2 15.0 1.0
ND1 C:HIS32 4.3 12.5 1.0
CE1 C:HIS236 4.3 17.5 1.0
CG C:HIS32 4.3 12.7 1.0
O C:HOH433 4.5 22.7 1.0
CB C:ASP302 4.6 13.0 1.0
CG C:PRO104 4.6 14.2 1.0
CG C:GLU175 4.6 19.9 1.0
O C:HOH363 4.7 27.1 1.0
NE2 C:HIS236 4.7 15.2 1.0
OH C:TYR134 4.8 19.3 1.0

Zinc binding site 6 out of 8 in 3k2g

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Zinc binding site 6 out of 8 in the Crystal Structure of A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides


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 A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:28.9
occ:1.00
O C:HOH364 2.1 13.1 1.0
OE1 C:GLU175 2.2 11.7 1.0
ND1 C:HIS207 2.3 16.7 1.0
NE2 C:HIS236 2.3 15.2 1.0
O C:HOH363 2.4 27.1 1.0
OH C:TYR134 2.7 19.3 1.0
CE1 C:HIS236 3.1 17.5 1.0
CE1 C:HIS207 3.1 16.4 1.0
CD C:GLU175 3.1 17.9 1.0
CG C:HIS207 3.4 16.2 1.0
OE2 C:GLU175 3.4 13.0 1.0
CD2 C:HIS236 3.5 18.2 1.0
ZN C:ZN400 3.5 15.5 1.0
CZ C:TYR134 3.7 23.7 1.0
CB C:HIS207 3.8 15.3 1.0
CE1 C:TYR134 3.9 23.0 1.0
O C:HOH869 4.0 29.8 1.0
ND1 C:HIS236 4.3 14.0 1.0
NE2 C:HIS207 4.3 18.0 1.0
CG C:GLU175 4.4 19.9 1.0
CD2 C:HIS207 4.5 17.7 1.0
NE2 C:HIS32 4.5 10.1 1.0
CE1 C:HIS32 4.5 13.1 1.0
CG C:HIS236 4.5 15.9 1.0
O3 C:DTV402 4.5 37.7 1.0
OD2 C:ASP302 4.6 15.7 1.0
CA C:HIS207 4.6 13.9 1.0
CE2 C:TYR134 5.0 23.0 1.0

Zinc binding site 7 out of 8 in 3k2g

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Zinc binding site 7 out of 8 in the Crystal Structure of A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides


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 A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn400

b:12.8
occ:1.00
O D:HOH365 2.1 18.3 1.0
NE2 D:HIS34 2.2 13.4 1.0
NE2 D:HIS32 2.2 11.2 1.0
OE2 D:GLU175 2.2 14.4 1.0
OD1 D:ASP302 2.2 8.3 1.0
CD2 D:HIS34 3.1 12.8 1.0
CD2 D:HIS32 3.1 10.8 1.0
CE1 D:HIS34 3.1 14.7 1.0
CG D:ASP302 3.2 12.4 1.0
CE1 D:HIS32 3.2 12.8 1.0
O D:HOH871 3.2 31.3 1.0
CD D:GLU175 3.3 22.3 1.0
OD2 D:ASP302 3.4 12.6 1.0
ZN D:ZN401 3.6 27.5 1.0
OE1 D:GLU175 3.7 18.7 1.0
ND1 D:HIS34 4.2 13.7 1.0
CE1 D:HIS236 4.3 20.0 1.0
CG D:HIS34 4.3 14.1 1.0
ND1 D:HIS32 4.3 11.9 1.0
CG D:HIS32 4.3 12.9 1.0
CG D:PRO104 4.5 14.6 1.0
CB D:ASP302 4.5 9.6 1.0
O D:HOH364 4.5 23.8 1.0
NE2 D:HIS236 4.5 20.3 1.0
CG D:GLU175 4.6 22.3 1.0
OH D:TYR134 4.8 26.5 1.0
O D:HOH414 4.9 18.1 1.0
CA D:ASP302 4.9 9.9 1.0

Zinc binding site 8 out of 8 in 3k2g

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Zinc binding site 8 out of 8 in the Crystal Structure of A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides


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 A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:27.5
occ:1.00
O D:HOH365 2.2 18.3 1.0
NE2 D:HIS236 2.3 20.3 1.0
ND1 D:HIS207 2.3 17.3 1.0
O D:HOH364 2.3 23.8 1.0
OE1 D:GLU175 2.4 18.7 1.0
OH D:TYR134 2.7 26.5 1.0
CE1 D:HIS236 3.1 20.0 1.0
CE1 D:HIS207 3.1 18.3 1.0
CD D:GLU175 3.2 22.3 1.0
CD2 D:HIS236 3.3 19.3 1.0
OE2 D:GLU175 3.4 14.4 1.0
CG D:HIS207 3.4 18.5 1.0
ZN D:ZN400 3.6 12.8 1.0
CZ D:TYR134 3.6 26.9 1.0
CE1 D:TYR134 3.8 25.2 1.0
CB D:HIS207 3.8 16.0 1.0
O D:HOH871 3.9 31.3 1.0
ND1 D:HIS236 4.3 17.0 1.0
NE2 D:HIS207 4.3 18.9 1.0
CG D:HIS236 4.4 17.4 1.0
CE1 D:HIS32 4.5 12.8 1.0
CD2 D:HIS207 4.5 18.1 1.0
OD2 D:ASP302 4.5 12.6 1.0
NE2 D:HIS32 4.5 11.2 1.0
CG D:GLU175 4.5 22.3 1.0
CA D:HIS207 4.6 16.2 1.0
O3 D:DTV402 4.7 38.8 1.0
CE2 D:TYR134 4.9 25.9 1.0
OD1 D:ASP302 5.0 8.3 1.0

Reference:

D.Kumaran, S.K.Burley, S.Swaminathan. Crystal Structure of A Resiniferatoxin-Binding Protein From Rhodobacter Sphaeroides To Be Published.
Page generated: Wed Dec 16 04:29:23 2020

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