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Zinc in PDB 2zcb: Crystal Structure of Ubiquitin P37A/P38A

Protein crystallography data

The structure of Crystal Structure of Ubiquitin P37A/P38A, PDB code: 2zcb was solved by R.Kitahara, T.Tanaka, E.Sakata, Y.Yamaguchi, K.Kato, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.786, 49.735, 93.168, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 22.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ubiquitin P37A/P38A (pdb code 2zcb). 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 Ubiquitin P37A/P38A, PDB code: 2zcb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 2zcb

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Zinc binding site 1 out of 5 in the Crystal Structure of Ubiquitin P37A/P38A


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 Ubiquitin P37A/P38A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn77

b:23.8
occ:1.00
CE1 A:HIS68 2.2 16.4 1.0
OD2 C:ASP39 2.2 28.3 1.0
O A:HOH87 2.4 30.0 1.0
NE2 A:HIS68 2.7 18.0 1.0
O C:HOH235 2.7 34.0 1.0
CG C:ASP39 2.9 25.3 1.0
OD1 C:ASP39 3.0 24.6 1.0
ND1 A:HIS68 3.3 19.3 1.0
CD2 A:HIS68 4.0 14.7 1.0
O A:HOH103 4.0 24.2 1.0
CB C:ASP39 4.3 22.0 1.0
CG A:HIS68 4.3 15.5 1.0
O C:HOH180 4.3 28.3 1.0
O A:HOH117 4.3 30.9 1.0
OE1 C:GLN40 4.4 31.6 1.0

Zinc binding site 2 out of 5 in 2zcb

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Zinc binding site 2 out of 5 in the Crystal Structure of Ubiquitin P37A/P38A


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 Ubiquitin P37A/P38A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn78

b:15.1
occ:1.00
OE1 A:GLU18 2.1 13.8 1.0
OE2 A:GLU18 2.8 15.0 1.0
CD A:GLU18 2.8 14.8 1.0
O A:HOH114 4.2 20.9 1.0
CG A:GLU18 4.2 14.9 1.0
O A:HOH125 4.5 31.1 1.0
O A:HOH147 4.8 50.1 1.0

Zinc binding site 3 out of 5 in 2zcb

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Zinc binding site 3 out of 5 in the Crystal Structure of Ubiquitin P37A/P38A


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 Ubiquitin P37A/P38A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn79

b:25.9
occ:1.00
OD1 A:ASP21 2.1 17.3 1.0
O A:HOH114 2.1 20.9 1.0
O A:HOH99 2.4 27.0 1.0
CG A:ASP21 2.7 17.4 1.0
OD2 A:ASP21 2.7 18.0 1.0
O A:HOH147 3.0 50.1 1.0
ND2 A:ASN25 3.9 11.8 1.0
CB A:ASP21 4.2 14.9 1.0
O A:HOH125 4.3 31.1 1.0
OE1 A:GLU18 4.4 13.8 1.0
CE A:LYS29 4.4 20.8 1.0
NZ A:LYS29 4.4 22.1 1.0
O A:HOH98 4.6 29.6 1.0
CG A:ASN25 4.7 13.5 1.0
CB A:ASN25 4.7 12.4 1.0
CA A:ASP21 4.8 14.6 1.0

Zinc binding site 4 out of 5 in 2zcb

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Zinc binding site 4 out of 5 in the Crystal Structure of Ubiquitin P37A/P38A


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 Ubiquitin P37A/P38A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn77

b:22.4
occ:1.00
NE2 C:HIS68 2.0 17.7 1.0
O B:HOH161 2.3 24.5 1.0
O B:HOH242 2.3 32.7 1.0
CE1 B:HIS68 2.4 22.9 1.0
CE1 C:HIS68 3.0 17.6 1.0
CD2 C:HIS68 3.0 18.3 1.0
O B:HOH227 3.1 43.4 1.0
NE2 B:HIS68 3.1 24.9 1.0
ND1 B:HIS68 3.2 24.1 1.0
NZ B:LYS6 4.1 34.5 1.0
ND1 C:HIS68 4.1 16.8 1.0
CG C:HIS68 4.1 15.6 1.0
CD2 B:HIS68 4.1 21.9 1.0
CG B:HIS68 4.2 21.5 1.0
O C:HOH183 4.3 23.9 1.0
CG2 C:THR66 4.5 15.3 1.0
O B:HOH229 4.7 33.4 1.0
O C:HOH211 4.7 45.9 1.0
CG B:LYS6 4.7 21.2 1.0
O B:HOH203 4.9 35.5 1.0
CB C:THR66 4.9 15.5 1.0

Zinc binding site 5 out of 5 in 2zcb

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Zinc binding site 5 out of 5 in the Crystal Structure of Ubiquitin P37A/P38A


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 Ubiquitin P37A/P38A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn78

b:18.0
occ:1.00
OE1 B:GLU18 2.1 18.3 1.0
OE2 B:GLU18 2.6 17.1 1.0
CD B:GLU18 2.7 16.3 1.0
O B:HOH177 3.9 37.2 1.0
O B:HOH155 4.0 17.3 1.0
CG B:GLU18 4.1 15.4 1.0
CB B:GLU18 4.9 12.4 1.0

Reference:

R.Kitahara, T.Tanaka, E.Sakata, Y.Yamaguchi, S.Yokoyama, K.Kato. Crystal Structure of Ubiquitin P37A/P38A To Be Published.
Page generated: Wed Dec 16 04:04:51 2020

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