Zinc in PDB 7kzz: Cryo-Em Structure of Yiip-Fab Complex in Holo State

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Yiip-Fab Complex in Holo State (pdb code 7kzz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of Yiip-Fab Complex in Holo State, PDB code: 7kzz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7kzz

Go back to Zinc Binding Sites List in 7kzz
Zinc binding site 1 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:93.9
occ:1.00
OD2 B:ASP287 1.7 67.8 1.0
NE2 B:HIS234 1.8 73.8 1.0
ND1 B:HIS250 1.9 71.2 1.0
CG B:HIS250 2.8 71.2 1.0
CD2 B:HIS234 2.8 73.8 1.0
CE1 B:HIS234 2.8 73.8 1.0
HB3 B:HIS250 2.9 71.2 1.0
CG B:ASP287 3.0 67.8 1.0
CE1 B:HIS250 3.0 71.2 1.0
HB2 B:HIS250 3.1 71.2 1.0
CB B:HIS250 3.1 71.2 1.0
HD2 B:HIS234 3.2 73.8 1.0
HE1 B:HIS234 3.2 73.8 1.0
HE1 B:HIS250 3.3 71.2 1.0
HB2 B:ASP287 3.7 67.8 1.0
OD1 B:ASP287 3.7 67.8 1.0
OD2 B:ASP235 3.8 76.9 1.0
HD2 B:HIS285 3.9 67.1 1.0
ND1 B:HIS234 3.9 73.8 1.0
CG B:HIS234 3.9 73.8 1.0
CB B:ASP287 3.9 67.8 1.0
CD2 B:HIS250 4.0 71.2 1.0
NE2 B:HIS250 4.0 71.2 1.0
HB3 B:ASP287 4.3 67.8 1.0
CA B:HIS250 4.6 71.2 1.0
CG B:ASP235 4.8 76.9 1.0
CD2 B:HIS285 4.8 67.1 1.0
HD1 B:HIS234 4.8 73.8 1.0
HB2 B:ASP235 4.9 76.9 1.0
HD2 B:HIS250 5.0 71.2 1.0
HE2 B:HIS250 5.0 71.2 1.0

Zinc binding site 2 out of 8 in 7kzz

Go back to Zinc Binding Sites List in 7kzz
Zinc binding site 2 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:127.8
occ:1.00
OD1 B:ASP70 1.7 104.4 1.0
OD2 B:ASP70 1.8 104.4 1.0
ND1 B:HIS73 1.9 98.9 1.0
NE2 B:HIS77 1.9 101.4 1.0
CG B:ASP70 2.2 104.4 1.0
HB2 B:HIS73 2.7 98.9 1.0
CG B:HIS73 2.8 98.9 1.0
CE1 B:HIS77 2.8 101.4 1.0
CD2 B:HIS77 3.0 101.4 1.0
CE1 B:HIS73 3.0 98.9 1.0
HE1 B:HIS77 3.1 101.4 1.0
CB B:HIS73 3.2 98.9 1.0
HD2 B:HIS77 3.3 101.4 1.0
HE1 B:HIS73 3.4 98.9 1.0
HB3 B:ASP72 3.5 100.7 1.0
CB B:ASP70 3.7 104.4 1.0
N B:HIS73 4.0 98.9 1.0
ND1 B:HIS77 4.0 101.4 1.0
H B:HIS73 4.0 98.9 1.0
CD2 B:HIS73 4.0 98.9 1.0
CG B:HIS77 4.0 101.4 1.0
HB3 B:HIS73 4.1 98.9 1.0
NE2 B:HIS73 4.1 98.9 1.0
HB3 B:ASP70 4.1 104.4 1.0
H B:ASP70 4.2 104.4 1.0
CA B:HIS73 4.2 98.9 1.0
HB2 B:ASP70 4.3 104.4 1.0
C B:ASP72 4.4 100.7 1.0
CB B:ASP72 4.6 100.7 1.0
OH B:TYR64 4.6 101.9 1.0
CA B:ASP70 4.6 104.4 1.0
H B:ASP72 4.6 100.7 1.0
N B:ASP70 4.7 104.4 1.0
O B:ASP70 4.7 104.4 1.0
C B:ASP70 4.9 104.4 1.0
HD1 B:HIS77 4.9 101.4 1.0
O B:ASP72 4.9 100.7 1.0
HD2 B:HIS73 5.0 98.9 1.0
CA B:ASP72 5.0 100.7 1.0
HA B:HIS73 5.0 98.9 1.0
O B:HIS73 5.0 98.9 1.0

Zinc binding site 3 out of 8 in 7kzz

Go back to Zinc Binding Sites List in 7kzz
Zinc binding site 3 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:158.1
occ:1.00
OD2 B:ASP51 1.7 119.8 1.0
OD1 B:ASP159 1.7 135.7 1.0
OD1 B:ASP47 1.8 119.3 1.0
OD2 B:ASP47 1.8 119.3 1.0
NE2 B:HIS155 2.0 137.6 1.0
CG B:ASP47 2.3 119.3 1.0
CG B:ASP159 2.9 135.7 1.0
CE1 B:HIS155 2.9 137.6 1.0
CG B:ASP51 3.0 119.8 1.0
HE1 B:HIS155 3.1 137.6 1.0
CD2 B:HIS155 3.2 137.6 1.0
OD2 B:ASP159 3.4 135.7 1.0
HD2 B:HIS155 3.5 137.6 1.0
OD1 B:ASP51 3.6 119.8 1.0
O B:ASP47 3.7 119.3 1.0
HA B:SER48 3.8 119.7 1.0
CB B:ASP47 3.8 119.3 1.0
HG B:SER48 3.8 119.7 1.0
HB2 B:ASP159 3.9 135.7 1.0
HD13 B:LEU162 4.0 125.5 1.0
C B:ASP47 4.0 119.3 1.0
CB B:ASP159 4.0 135.7 1.0
HB2 B:ASP51 4.1 119.8 1.0
ND1 B:HIS155 4.1 137.6 1.0
CB B:ASP51 4.1 119.8 1.0
CG B:HIS155 4.3 137.6 1.0
HB3 B:ASP47 4.3 119.3 1.0
HB2 B:ASP47 4.3 119.3 1.0
CA B:ASP47 4.5 119.3 1.0
N B:SER48 4.5 119.7 1.0
H B:ASP51 4.5 119.8 1.0
HB3 B:ASP159 4.6 135.7 1.0
HA B:ASP47 4.6 119.3 1.0
HD1 B:TYR156 4.6 142.8 1.0
CA B:SER48 4.6 119.7 1.0
HD22 B:ASN163 4.8 129.4 1.0
OG B:SER48 4.8 119.7 1.0
HB3 B:ASP51 4.9 119.8 1.0
CD1 B:LEU162 4.9 125.5 1.0
HA B:ASP159 5.0 135.7 1.0

Zinc binding site 4 out of 8 in 7kzz

Go back to Zinc Binding Sites List in 7kzz
Zinc binding site 4 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:105.1
occ:1.00
OD1 A:ASP287 1.8 67.3 1.0
OD2 B:ASP267 1.8 72.4 1.0
OD1 B:ASP267 1.8 72.4 1.0
NE2 B:HIS263 1.9 64.4 1.0
NE2 A:HIS285 2.0 66.9 1.0
CG B:ASP267 2.3 72.4 1.0
CE1 B:HIS263 2.8 64.4 1.0
CE1 A:HIS285 2.9 66.9 1.0
CD2 B:HIS263 3.0 64.4 1.0
HE1 A:HIS285 3.0 66.9 1.0
CG A:ASP287 3.1 67.3 1.0
HE1 B:HIS263 3.1 64.4 1.0
CD2 A:HIS285 3.2 66.9 1.0
HD2 B:HIS263 3.3 64.4 1.0
HD2 A:HIS285 3.5 66.9 1.0
HA A:ASP287 3.7 67.3 1.0
OD2 A:ASP287 3.8 67.3 1.0
CB B:ASP267 3.8 72.4 1.0
ND1 B:HIS263 4.0 64.4 1.0
CG B:HIS263 4.0 64.4 1.0
ND1 A:HIS285 4.1 66.9 1.0
HB2 B:ASP267 4.1 72.4 1.0
CB A:ASP287 4.2 67.3 1.0
CG A:HIS285 4.2 66.9 1.0
HB3 B:ASP267 4.4 72.4 1.0
CA A:ASP287 4.4 67.3 1.0
HD2 A:PRO288 4.5 65.4 1.0
HB3 A:ASP287 4.5 67.3 1.0
H B:ASP267 4.8 72.4 1.0
CA B:ASP267 4.8 72.4 1.0
HG22 B:THR266 4.8 65.9 1.0
HA B:ASP267 4.8 72.4 1.0
HD1 B:HIS263 4.9 64.4 1.0
N A:ASP287 4.9 67.3 1.0
HB B:THR266 4.9 65.9 1.0
N B:ASP267 4.9 72.4 1.0
HD1 A:HIS285 5.0 66.9 1.0

Zinc binding site 5 out of 8 in 7kzz

Go back to Zinc Binding Sites List in 7kzz
Zinc binding site 5 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:107.1
occ:1.00
OD1 B:ASP287 1.8 67.8 1.0
OD2 A:ASP267 1.8 72.8 1.0
OD1 A:ASP267 1.8 72.8 1.0
NE2 A:HIS263 1.9 64.5 1.0
NE2 B:HIS285 2.0 67.1 1.0
CG A:ASP267 2.3 72.8 1.0
CE1 A:HIS263 2.8 64.5 1.0
CE1 B:HIS285 2.9 67.1 1.0
CD2 A:HIS263 3.0 64.5 1.0
HE1 B:HIS285 3.0 67.1 1.0
CG B:ASP287 3.1 67.8 1.0
HE1 A:HIS263 3.1 64.5 1.0
CD2 B:HIS285 3.2 67.1 1.0
HD2 A:HIS263 3.3 64.5 1.0
HD2 B:HIS285 3.5 67.1 1.0
HA B:ASP287 3.7 67.8 1.0
OD2 B:ASP287 3.8 67.8 1.0
CB A:ASP267 3.8 72.8 1.0
ND1 A:HIS263 4.0 64.5 1.0
CG A:HIS263 4.0 64.5 1.0
ND1 B:HIS285 4.1 67.1 1.0
HB2 A:ASP267 4.1 72.8 1.0
CB B:ASP287 4.2 67.8 1.0
CG B:HIS285 4.2 67.1 1.0
HB3 A:ASP267 4.4 72.8 1.0
CA B:ASP287 4.4 67.8 1.0
HD2 B:PRO288 4.5 65.4 1.0
HB3 B:ASP287 4.5 67.8 1.0
H A:ASP267 4.8 72.8 1.0
HG22 A:THR266 4.8 66.1 1.0
CA A:ASP267 4.8 72.8 1.0
HA A:ASP267 4.8 72.8 1.0
HD1 A:HIS263 4.9 64.5 1.0
HB A:THR266 4.9 66.1 1.0
HD1 B:HIS285 4.9 67.1 1.0
N A:ASP267 4.9 72.8 1.0
N B:ASP287 5.0 67.8 1.0

Zinc binding site 6 out of 8 in 7kzz

Go back to Zinc Binding Sites List in 7kzz
Zinc binding site 6 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:95.0
occ:1.00
OD2 A:ASP287 1.7 67.3 1.0
NE2 A:HIS234 1.8 73.6 1.0
ND1 A:HIS250 1.9 70.6 1.0
CD2 A:HIS234 2.8 73.6 1.0
CG A:HIS250 2.8 70.6 1.0
CE1 A:HIS234 2.9 73.6 1.0
HB3 A:HIS250 2.9 70.6 1.0
CE1 A:HIS250 3.0 70.6 1.0
CG A:ASP287 3.0 67.3 1.0
HB2 A:HIS250 3.1 70.6 1.0
HD2 A:HIS234 3.1 73.6 1.0
CB A:HIS250 3.2 70.6 1.0
HE1 A:HIS234 3.3 73.6 1.0
HE1 A:HIS250 3.3 70.6 1.0
HB2 A:ASP287 3.7 67.3 1.0
OD1 A:ASP287 3.7 67.3 1.0
OD2 A:ASP235 3.8 76.8 1.0
HD2 A:HIS285 3.9 66.9 1.0
CG A:HIS234 3.9 73.6 1.0
CB A:ASP287 3.9 67.3 1.0
ND1 A:HIS234 3.9 73.6 1.0
CD2 A:HIS250 4.0 70.6 1.0
NE2 A:HIS250 4.0 70.6 1.0
HB3 A:ASP287 4.3 67.3 1.0
CA A:HIS250 4.7 70.6 1.0
CG A:ASP235 4.8 76.8 1.0
CD2 A:HIS285 4.8 66.9 1.0
HD1 A:HIS234 4.9 73.6 1.0
HB2 A:ASP235 4.9 76.8 1.0
HE2 A:HIS250 5.0 70.6 1.0
HD2 A:HIS250 5.0 70.6 1.0

Zinc binding site 7 out of 8 in 7kzz

Go back to Zinc Binding Sites List in 7kzz
Zinc binding site 7 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:128.2
occ:1.00
OD1 A:ASP72 1.8 101.3 1.0
OD1 A:ASP70 1.8 104.9 1.0
OD2 A:ASP70 1.8 104.9 1.0
ND1 A:HIS73 2.0 98.7 1.0
CG A:ASP70 2.2 104.9 1.0
NE2 A:HIS77 2.3 101.5 1.0
HB2 A:HIS73 2.8 98.7 1.0
CG A:HIS73 2.9 98.7 1.0
CG A:ASP72 3.0 101.3 1.0
CE1 A:HIS73 3.0 98.7 1.0
CE1 A:HIS77 3.2 101.5 1.0
CB A:HIS73 3.3 98.7 1.0
CD2 A:HIS77 3.3 101.5 1.0
HE1 A:HIS77 3.4 101.5 1.0
HE1 A:HIS73 3.4 98.7 1.0
H A:HIS73 3.5 98.7 1.0
OD2 A:ASP72 3.6 101.3 1.0
N A:HIS73 3.6 98.7 1.0
HD2 A:HIS77 3.7 101.5 1.0
H A:ASP72 3.7 101.3 1.0
CB A:ASP70 3.7 104.9 1.0
C A:ASP72 4.0 101.3 1.0
CD2 A:HIS73 4.1 98.7 1.0
CA A:HIS73 4.1 98.7 1.0
NE2 A:HIS73 4.1 98.7 1.0
CB A:ASP72 4.2 101.3 1.0
HB2 A:ASP70 4.2 104.9 1.0
HB3 A:ASP70 4.2 104.9 1.0
HB3 A:HIS73 4.3 98.7 1.0
H A:ASP70 4.3 104.9 1.0
ND1 A:HIS77 4.3 101.5 1.0
N A:ASP72 4.4 101.3 1.0
CA A:ASP72 4.4 101.3 1.0
CG A:HIS77 4.4 101.5 1.0
CA A:ASP70 4.6 104.9 1.0
HB2 A:ASP72 4.6 101.3 1.0
O A:ASP72 4.7 101.3 1.0
C A:ASP70 4.7 104.9 1.0
HD2 A:HIS71 4.7 103.6 1.0
N A:ASP70 4.8 104.9 1.0
O A:ASP70 4.8 104.9 1.0
HA A:HIS73 4.8 98.7 1.0

Zinc binding site 8 out of 8 in 7kzz

Go back to Zinc Binding Sites List in 7kzz
Zinc binding site 8 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:156.4
occ:1.00
OD2 A:ASP51 1.7 118.9 1.0
OD1 A:ASP159 1.7 134.8 1.0
OD1 A:ASP47 1.8 118.4 1.0
OD2 A:ASP47 1.8 118.4 1.0
NE2 A:HIS155 2.0 137.1 1.0
CG A:ASP47 2.3 118.4 1.0
CG A:ASP159 2.9 134.8 1.0
CG A:ASP51 3.0 118.9 1.0
CE1 A:HIS155 3.0 137.1 1.0
CD2 A:HIS155 3.1 137.1 1.0
HE1 A:HIS155 3.2 137.1 1.0
HD2 A:HIS155 3.4 137.1 1.0
OD2 A:ASP159 3.5 134.8 1.0
OD1 A:ASP51 3.6 118.9 1.0
HG A:SER48 3.7 118.9 1.0
HA A:SER48 3.7 118.9 1.0
CB A:ASP47 3.8 118.4 1.0
O A:ASP47 3.8 118.4 1.0
HB2 A:ASP159 3.9 134.8 1.0
HD13 A:LEU162 3.9 124.9 1.0
HB2 A:ASP51 4.0 118.9 1.0
CB A:ASP159 4.0 134.8 1.0
C A:ASP47 4.1 118.4 1.0
CB A:ASP51 4.1 118.9 1.0
ND1 A:HIS155 4.1 137.1 1.0
CG A:HIS155 4.2 137.1 1.0
HB2 A:ASP47 4.3 118.4 1.0
HB3 A:ASP47 4.3 118.4 1.0
N A:SER48 4.4 118.9 1.0
CA A:ASP47 4.5 118.4 1.0
CA A:SER48 4.6 118.9 1.0
H A:ASP51 4.7 118.9 1.0
HB3 A:ASP159 4.7 134.8 1.0
OG A:SER48 4.7 118.9 1.0
HA A:ASP47 4.7 118.4 1.0
CD1 A:LEU162 4.8 124.9 1.0
HD1 A:TYR156 4.8 142.7 1.0
HB3 A:ASP51 4.8 118.9 1.0
HD12 A:LEU162 4.9 124.9 1.0
HA A:ASP159 4.9 134.8 1.0
HD22 A:ASN163 4.9 128.0 1.0
HD11 A:LEU162 5.0 124.9 1.0
H A:SER48 5.0 118.9 1.0

Reference:

M.L.Lopez-Redondo, S.Fan, A.Koide, S.Koide, O.Beckstein, D.L.Stokes. Cryo-Em Structure of Yiip-Fab Complex in Holo State To Be Published.
Page generated: Mon Jan 25 16:48:08 2021

Last articles

Zn in 7L3L
Zn in 7KSO
Zn in 7KSR
Zn in 7KTP
Zn in 7LMM
Zn in 7LMK
Zn in 7LLZ
Zn in 7LLF
Zn in 7L0N
Zn in 7LBR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy