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Zinc in PDB 5xwd: Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd

Enzymatic activity of Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd

All present enzymatic activity of Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd, PDB code: 5xwd was solved by T.Matsuda, T.Ito, M.Shirouzu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.49 / 2.89
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 203.428, 203.428, 113.817, 90.00, 90.00, 120.00
R / Rfree (%) 27.7 / 33.1

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd (pdb code 5xwd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 20 binding sites of Zinc where determined in the Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd, PDB code: 5xwd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 20 in 5xwd

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Zinc binding site 1 out of 20 in the Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd


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 the Complex of 059-152-Fv and Egfr-Ecd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn715

b:0.0
occ:1.00
OE2 A:GLU21 2.3 0.6 1.0
CD A:GLU21 2.4 0.5 1.0
OE1 A:GLU21 2.9 0.7 1.0
CG A:GLU21 3.2 0.8 1.0
CB A:GLU21 4.1 93.5 1.0
CD1 A:LEU25 4.6 87.0 1.0
OD1 A:ASP22 4.6 91.5 1.0

Zinc binding site 2 out of 20 in 5xwd

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Zinc binding site 2 out of 20 in the Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd


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 the Complex of 059-152-Fv and Egfr-Ecd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn716

b:0.4
occ:1.00
ND1 A:HIS121 2.7 88.0 1.0
CE1 A:HIS121 3.1 90.7 1.0
O A:LEU120 3.6 80.3 1.0
OD2 A:ASP147 3.9 94.2 1.0
CG A:HIS121 4.0 80.3 1.0
OG A:SER145 4.1 0.9 1.0
NE2 A:HIS121 4.3 77.2 1.0
C A:LEU120 4.4 75.0 1.0
OD1 A:ASP147 4.5 0.9 1.0
CE2 A:PHE148 4.6 85.6 1.0
CG A:ASP147 4.6 0.7 1.0
CB A:HIS121 4.6 78.5 1.0
CA A:HIS121 4.7 80.3 1.0
CB A:SER145 4.7 93.5 1.0
CD2 A:HIS121 4.8 75.4 1.0
N A:HIS121 4.9 73.0 1.0

Zinc binding site 3 out of 20 in 5xwd

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Zinc binding site 3 out of 20 in the Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd


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 the Complex of 059-152-Fv and Egfr-Ecd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn717

b:0.3
occ:1.00
ZN A:ZN728 1.9 0.8 1.0
OE1 A:GLN252 2.1 0.8 1.0
NE2 A:HIS566 2.1 0.8 1.0
CD A:GLN252 2.7 0.5 1.0
CE1 A:HIS566 3.0 0.8 1.0
CB A:GLN252 3.0 0.3 1.0
CD2 A:HIS566 3.1 0.5 1.0
CG A:GLN252 3.2 0.2 1.0
NE2 A:GLN252 3.7 0.0 1.0
O A:THR250 3.8 0.2 1.0
OD2 A:ASP553 3.9 0.5 1.0
ND1 A:HIS566 4.1 0.2 1.0
CG A:HIS566 4.2 91.7 1.0
CA A:GLN252 4.4 1.0 1.0
OD1 A:ASP553 4.5 0.0 1.0
CG A:ASP553 4.6 0.8 1.0
O A:TYR251 4.7 0.1 1.0
N A:GLN252 4.8 0.1 1.0
C A:TYR251 4.8 0.9 1.0
C A:THR250 5.0 0.7 1.0

Zinc binding site 4 out of 20 in 5xwd

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Zinc binding site 4 out of 20 in the Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd


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 the Complex of 059-152-Fv and Egfr-Ecd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn718

b:0.8
occ:1.00
ZN A:ZN729 2.0 0.6 1.0
OD2 A:ASP279 2.1 0.7 1.0
CG A:ASP279 2.8 0.8 1.0
OD1 A:ASP279 3.0 0.4 1.0
ND1 A:HIS280 3.2 0.5 1.0
CE1 A:HIS280 3.5 0.1 1.0
NZ A:LYS304 3.7 0.8 1.0
N A:ASP279 3.8 0.3 1.0
CE A:LYS304 3.9 0.6 1.0
ZN A:ZN727 3.9 0.4 1.0
CB A:THR278 3.9 0.4 1.0
CB A:ASP279 4.1 0.9 1.0
CG A:HIS280 4.4 0.0 1.0
N A:HIS280 4.4 0.0 1.0
CA A:ASP279 4.4 0.7 1.0
CG2 A:THR278 4.4 0.2 1.0
OG1 A:THR278 4.6 97.7 1.0
CA A:THR278 4.7 0.2 1.0
C A:THR278 4.7 1.0 1.0
C A:ASP279 4.8 0.8 1.0
NE2 A:HIS280 4.8 0.2 1.0
CB A:HIS280 5.0 0.1 1.0

Zinc binding site 5 out of 20 in 5xwd

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Zinc binding site 5 out of 20 in the Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd


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 the Complex of 059-152-Fv and Egfr-Ecd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn719

b:0.8
occ:1.00
NE2 A:HIS334 2.3 0.4 1.0
ZN A:ZN725 2.7 0.7 1.0
CD2 A:HIS334 2.9 0.2 1.0
CE1 A:HIS334 3.5 0.6 1.0
O A:THR330 4.0 0.6 1.0
CG A:HIS334 4.1 0.8 1.0
C8 A:NAG705 4.1 0.8 1.0
ND1 A:HIS334 4.4 0.2 1.0
CA A:ASN331 4.4 0.1 1.0
C6 A:NAG704 4.6 0.1 1.0
CB A:ASN331 4.7 0.5 1.0
C A:THR330 4.7 0.5 1.0
CG2 A:THR330 4.8 94.0 1.0
N A:ASN331 4.9 93.3 1.0
OE1 A:GLU320 4.9 0.7 1.0

Zinc binding site 6 out of 20 in 5xwd

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Zinc binding site 6 out of 20 in the Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd


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 the Complex of 059-152-Fv and Egfr-Ecd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn720

b:0.4
occ:1.00
OD1 A:ASP369 2.1 0.3 1.0
NH1 A:ARG390 2.1 0.3 1.0
ND1 A:HIS394 2.6 0.8 1.0
CG A:ASP369 3.2 1.0 1.0
CG A:HIS394 3.4 0.4 1.0
CZ A:ARG390 3.4 0.5 1.0
CB A:HIS394 3.4 95.4 1.0
CE1 A:HIS394 3.6 0.4 1.0
OD2 A:ASP369 3.7 0.9 1.0
N A:ALA395 3.9 87.9 1.0
C A:HIS394 4.1 93.9 1.0
NH2 A:ARG390 4.1 0.6 1.0
NE A:ARG390 4.2 0.2 1.0
CB A:ALA395 4.3 83.8 1.0
CA A:HIS394 4.3 93.1 1.0
CD A:ARG390 4.3 0.3 1.0
CA A:ALA395 4.3 80.4 1.0
CB A:ASP369 4.4 97.2 1.0
CD2 A:HIS394 4.5 0.9 1.0
CA A:ASP369 4.6 96.7 1.0
NE2 A:HIS394 4.6 0.8 1.0
O A:HIS394 4.7 93.0 1.0
N A:ASP369 4.7 99.2 1.0
N A:HIS394 4.9 86.9 1.0

Zinc binding site 7 out of 20 in 5xwd

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Zinc binding site 7 out of 20 in the Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd


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 the Complex of 059-152-Fv and Egfr-Ecd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn721

b:0.9
occ:1.00
ZN A:ZN726 2.1 0.1 1.0
NE2 A:HIS560 2.2 88.8 1.0
CE1 A:HIS560 2.6 87.6 1.0
CD2 A:HIS560 3.4 92.0 1.0
ND1 A:HIS560 3.7 88.3 1.0
CG A:HIS560 4.1 92.0 1.0
O A:ALA559 4.6 82.6 1.0
CB A:ALA559 4.8 82.9 1.0

Zinc binding site 8 out of 20 in 5xwd

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Zinc binding site 8 out of 20 in the Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd


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 the Complex of 059-152-Fv and Egfr-Ecd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn722

b:0.4
occ:1.00
OD2 A:ASP392 2.3 97.0 1.0
OD1 A:ASP392 3.0 99.5 1.0
CG A:ASP392 3.0 94.0 1.0
NH2 A:ARG427 3.1 1.0 1.0
CD2 A:HIS394 3.7 0.9 1.0
CB A:HIS394 4.1 95.4 1.0
CG A:HIS394 4.3 0.4 1.0
CA A:HIS394 4.3 93.1 1.0
CZ A:ARG427 4.3 0.2 1.0
CB A:ASP392 4.5 78.5 1.0
NE A:ARG427 4.8 0.7 1.0
OE2 A:GLU397 4.9 0.2 1.0
N A:HIS394 4.9 86.9 1.0
NE2 A:HIS394 4.9 0.8 1.0

Zinc binding site 9 out of 20 in 5xwd

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Zinc binding site 9 out of 20 in the Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn723

b:0.5
occ:1.00
OD1 A:ASP513 2.9 0.9 1.0
OD2 A:ASP513 3.3 94.2 1.0
CG A:ASP513 3.5 97.0 1.0
CG2 A:VAL512 4.0 0.8 1.0
NZ A:LYS514 4.3 0.5 1.0
NH2 A:ARG507 4.5 95.1 1.0
O A:LYS514 4.5 93.4 1.0
CG A:LYS514 5.0 90.4 1.0

Zinc binding site 10 out of 20 in 5xwd

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Zinc binding site 10 out of 20 in the Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Complex of 059-152-Fv and Egfr-Ecd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn724

b:0.8
occ:1.00
ND1 A:HIS594 2.2 0.0 1.0
CE1 A:HIS594 3.1 0.9 1.0
CG A:HIS594 3.2 0.7 1.0
CB A:HIS594 3.5 99.3 1.0
CA A:HIS594 3.8 95.0 1.0
N A:LEU595 3.9 89.7 1.0
NE2 A:HIS594 4.2 0.7 1.0
CD2 A:HIS594 4.2 91.7 1.0
C A:HIS594 4.4 93.3 1.0
O A:CYS593 4.9 81.7 1.0
CB A:LEU595 5.0 83.5 1.0

Reference:

T.Matsuda, T.Ito, C.Takemoto, K.Katsura, M.Ikeda, M.Wakiyama, M.Kukimoto-Niino, S.Yokoyama, Y.Kurosawa, M.Shirouzu. Cell-Free Synthesis of Functional Antibody Fragments to Provide A Structural Basis For Antibody-Antigen Interaction Plos One V. 13 93158 2018.
ISSN: ESSN 1932-6203
PubMed: 29462206
DOI: 10.1371/JOURNAL.PONE.0193158
Page generated: Wed Dec 16 11:21:19 2020

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