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 7RE3
Zn in 7RDX
Zn in 7RDZ
Zn in 7RWM
Zn in 7PGU
Zn in 7PGR
Zn in 7PGT
Zn in 7PGS
Zn in 7SQE
Zn in 7RWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy