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

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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

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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

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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

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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

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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

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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

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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

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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

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