Zinc in PDB 7wn8: Crystal Structure of Antibody (BC31M5) Binds to CD47

Protein crystallography data

The structure of Crystal Structure of Antibody (BC31M5) Binds to CD47, PDB code: 7wn8 was solved by Y.Li, W.Wang, J.Sui, S.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.59 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.402, 94.281, 174.929, 90, 90, 90
R / Rfree (%) 24.3 / 27.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Antibody (BC31M5) Binds to CD47 (pdb code 7wn8). 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 Antibody (BC31M5) Binds to CD47, PDB code: 7wn8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7wn8

Go back to Zinc Binding Sites List in 7wn8
Zinc binding site 1 out of 8 in the Crystal Structure of Antibody (BC31M5) Binds to CD47


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 Antibody (BC31M5) Binds to CD47 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:34.7
occ:1.00
 OE2 A:GLU122 1.9 34.2 1.0
NE2 L:HIS92 2.3 35.3 1.0
O L:HOH410 2.4 35.6 1.0
CE1 L:HIS92 2.5 35.2 1.0
O A:HOH519 2.5 42.8 1.0
CD A:GLU122 2.9 34.8 1.0
OE1 A:GLU122 3.3 35.4 1.0
CD2 L:HIS92 3.6 35.6 1.0
OD1 L:ASN95 3.8 43.0 1.0
ND1 L:HIS92 3.8 34.7 1.0
N L:ASN95 3.9 39.4 1.0
CG A:GLU122 4.3 34.1 1.0
CG L:HIS92 4.4 34.7 1.0
CA L:ASN95 4.5 39.0 1.0
CZ2 L:TRP97 4.6 33.1 1.0
N L:GLN94 4.7 40.8 1.0
CH2 L:TRP97 4.8 34.0 1.0
CA L:GLN94 4.8 42.5 1.0
CG L:ASN95 4.9 41.8 1.0
C L:GLN94 4.9 40.9 1.0

Zinc binding site 2 out of 8 in 7wn8

Go back to Zinc Binding Sites List in 7wn8
Zinc binding site 2 out of 8 in the Crystal Structure of Antibody (BC31M5) Binds to CD47


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 Antibody (BC31M5) Binds to CD47 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:214.2
occ:1.00
 O A:HOH521 2.3 59.8 1.0
OE2 A:GLU115 2.3 57.9 1.0
NZ A:LYS59 2.4 66.4 1.0
OE1 A:GLU124 3.2 58.3 1.0
CD A:GLU115 3.3 54.4 1.0
CE A:LYS59 3.3 64.0 1.0
CG A:GLU115 3.5 52.8 1.0
CE1 L:HIS33 3.9 43.5 1.0
O A:HOH502 4.2 58.0 1.0
O A:HOH519 4.2 42.8 1.0
CB A:GLU115 4.3 51.7 1.0
NZ A:LYS57 4.4 53.0 1.0
CD A:GLU124 4.4 55.9 1.0
NE2 L:HIS33 4.4 42.6 1.0
OE1 A:GLU115 4.4 51.4 1.0
CD A:LYS59 4.7 61.5 1.0
CE A:LYS57 4.8 53.4 1.0
OE2 A:GLU124 4.9 57.4 1.0

Zinc binding site 3 out of 8 in 7wn8

Go back to Zinc Binding Sites List in 7wn8
Zinc binding site 3 out of 8 in the Crystal Structure of Antibody (BC31M5) Binds to CD47


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 Antibody (BC31M5) Binds to CD47 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:168.8
occ:1.00
 CE1 A:HIS108 1.8 84.8 1.0
OD2 A:ASP80 2.2 81.8 1.0
NE2 A:HIS108 2.3 81.3 1.0
O A:HOH516 2.6 91.1 1.0
ND1 A:HIS108 3.0 77.4 1.0
CG A:ASP80 3.4 77.9 1.0
CD2 A:HIS108 3.6 75.9 1.0
NH2 A:ARG63 3.7 76.4 1.0
CG A:HIS108 3.9 73.5 1.0
CB A:ASP80 4.2 76.3 1.0
OD1 A:ASP80 4.4 74.5 1.0
CZ A:ARG63 4.6 73.7 1.0
NH1 A:ARG63 4.8 72.0 1.0

Zinc binding site 4 out of 8 in 7wn8

Go back to Zinc Binding Sites List in 7wn8
Zinc binding site 4 out of 8 in the Crystal Structure of Antibody (BC31M5) Binds to CD47


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 Antibody (BC31M5) Binds to CD47 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:30.8
occ:1.00
 OE1 A:GLU47 2.0 34.2 1.0
CD A:GLU47 2.8 35.0 1.0
OE2 A:GLU47 3.0 34.4 1.0
CG A:GLU47 4.2 35.7 1.0
CB A:GLU47 4.7 35.5 1.0

Zinc binding site 5 out of 8 in 7wn8

Go back to Zinc Binding Sites List in 7wn8
Zinc binding site 5 out of 8 in the Crystal Structure of Antibody (BC31M5) Binds to CD47


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 Antibody (BC31M5) Binds to CD47 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:43.1
occ:1.00
 O Q:HOH301 2.1 44.6 1.0
OE1 C:GLU122 2.1 39.3 1.0
OE2 C:GLU122 2.2 45.8 1.0
NE2 Q:HIS92 2.3 40.8 1.0
CD C:GLU122 2.4 43.1 1.0
CE1 Q:HIS92 2.6 40.4 1.0
OD1 Q:ASN95 3.6 44.0 1.0
CD2 Q:HIS92 3.6 40.3 1.0
O C:HOH501 3.8 44.1 1.0
ND1 Q:HIS92 3.9 40.5 1.0
O C:HOH518 3.9 35.6 1.0
CG C:GLU122 3.9 44.2 1.0
N Q:ASN95 4.1 44.2 1.0
CG Q:HIS92 4.4 40.5 1.0
CA Q:ASN95 4.4 44.8 1.0
CH2 Q:TRP97 4.6 39.8 1.0
CZ2 Q:TRP97 4.6 39.1 1.0
CB C:GLU122 4.7 41.0 1.0
CG2 P:THR100 4.7 37.2 1.0
CG Q:ASN95 4.7 46.3 1.0

Zinc binding site 6 out of 8 in 7wn8

Go back to Zinc Binding Sites List in 7wn8
Zinc binding site 6 out of 8 in the Crystal Structure of Antibody (BC31M5) Binds to CD47


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 Antibody (BC31M5) Binds to CD47 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:34.2
occ:1.00
 OE1 C:GLU47 2.0 38.4 1.0
OE2 C:GLU47 2.2 36.9 1.0
CD C:GLU47 2.3 38.2 1.0
O P:HOH431 3.2 13.0 1.0
CG C:GLU47 3.8 37.9 1.0
CB C:GLU47 4.7 39.0 1.0
O C:HOH505 4.9 42.2 1.0

Zinc binding site 7 out of 8 in 7wn8

Go back to Zinc Binding Sites List in 7wn8
Zinc binding site 7 out of 8 in the Crystal Structure of Antibody (BC31M5) Binds to CD47


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 Antibody (BC31M5) Binds to CD47 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn301

b:56.1
occ:1.00
 O H:HOH305 2.3 45.7 1.0
NE2 H:HIS167 2.3 43.7 1.0
OD1 L:ASN138 2.3 46.1 1.0
ND2 L:ASN139 2.7 44.5 1.0
CD2 H:HIS167 2.8 43.4 1.0
O L:HOH431 2.8 44.9 1.0
O L:HOH413 2.8 46.4 1.0
OD1 L:ASN139 2.9 43.3 1.0
CG L:ASN138 3.0 43.0 1.0
CG L:ASN139 3.0 43.1 1.0
ND2 L:ASN138 3.0 43.5 1.0
CE1 H:HIS167 3.5 43.8 1.0
CG H:HIS167 4.1 43.5 1.0
OG L:SER175 4.1 40.0 1.0
O H:GLY165 4.4 47.1 1.0
CB L:ASN139 4.4 41.0 1.0
ND1 H:HIS167 4.4 43.7 1.0
CB L:ASN138 4.5 41.2 1.0
CA H:GLY165 4.5 48.5 1.0
OG1 H:THR186 4.6 48.9 1.0
N L:ASN139 4.7 40.2 1.0
C H:GLY165 4.7 48.2 1.0
CA L:ASN139 5.0 40.6 1.0

Zinc binding site 8 out of 8 in 7wn8

Go back to Zinc Binding Sites List in 7wn8
Zinc binding site 8 out of 8 in the Crystal Structure of Antibody (BC31M5) Binds to CD47


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 Antibody (BC31M5) Binds to CD47 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn301

b:58.7
occ:1.00
 O Q:HOH304 2.0 46.8 1.0
CE1 P:HIS167 2.2 51.4 1.0
OD1 Q:ASN139 2.8 51.4 1.0
OD1 Q:ASN138 2.9 47.7 1.0
NE2 P:HIS167 3.1 50.0 1.0
ND1 P:HIS167 3.2 50.2 1.0
ND2 Q:ASN138 3.4 47.8 1.0
CG Q:ASN138 3.6 46.6 1.0
CA P:GLY165 3.6 55.4 1.0
O P:GLY165 3.6 54.0 1.0
OG1 P:THR186 3.6 53.2 1.0
CG Q:ASN139 3.7 47.5 1.0
ND2 Q:ASN139 3.8 47.2 1.0
C P:GLY165 4.0 54.6 1.0
CD2 P:HIS167 4.3 49.5 1.0
CG P:HIS167 4.3 50.0 1.0
N P:GLY165 4.7 56.0 1.0
CB P:THR186 4.9 54.2 1.0

Reference:

Y.Li, W.Wang, S.Zheng, J.Sui. Crystal Structure of Antibody BC31M5 Binds to Leukocyte Surface Antigen CD47. To Be Published.
Page generated: Wed Oct 30 14:26:31 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy