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Zinc in PDB 2p46: Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold.

Enzymatic activity of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold.

All present enzymatic activity of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold.:
3.1.27.5;

Protein crystallography data

The structure of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold., PDB code: 2p46 was solved by V.Tereshko, S.Uysal, A.Koide, K.Margalef, S.Koide, A.A.Kossiakoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.270, 70.057, 123.408, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 29.9

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold. (pdb code 2p46). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold., PDB code: 2p46:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in 2p46

Go back to Zinc Binding Sites List in 2p46
Zinc binding site 1 out of 13 in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:32.4
occ:0.50
 ZN A:ZN201 0.0 32.4 0.5
NE2 A:HIS12 2.2 28.2 1.0
CD2 A:HIS12 3.0 28.5 1.0
CE1 A:HIS12 3.3 28.4 1.0
ZN A:ZN201 3.4 33.7 0.5
OE1 A:GLN11 3.5 38.1 1.0
N A:PHE120 4.2 29.5 1.0
CD A:GLN11 4.2 33.8 1.0
CG A:HIS12 4.3 29.9 1.0
CB A:PHE120 4.3 29.2 1.0
ND1 A:HIS12 4.4 26.1 1.0
CB A:GLN11 4.4 33.5 1.0
O A:PHE120 4.6 28.8 1.0
CG A:GLN11 4.7 33.6 1.0
NZ A:LYS41 4.7 32.2 0.5
CA A:PHE120 4.8 29.2 1.0
OD1 A:ASN44 4.9 32.0 1.0

Zinc binding site 2 out of 13 in 2p46

Go back to Zinc Binding Sites List in 2p46
Zinc binding site 2 out of 13 in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:33.7
occ:0.50
 ZN A:ZN201 0.0 33.7 0.5
ND1 A:HIS119 2.3 30.4 1.0
CE1 A:HIS119 3.2 31.3 1.0
CG A:HIS119 3.3 30.6 1.0
ZN A:ZN201 3.4 32.4 0.5
CB A:HIS119 3.6 28.6 1.0
CA A:HIS119 3.7 28.8 1.0
N A:PHE120 4.0 29.5 1.0
C A:HIS119 4.3 29.2 1.0
NE2 A:HIS119 4.4 33.0 1.0
CD2 A:HIS119 4.4 31.5 1.0
O A:PHE120 4.5 28.8 1.0
O A:VAL118 4.6 28.0 1.0
N A:HIS119 4.9 28.2 1.0

Zinc binding site 3 out of 13 in 2p46

Go back to Zinc Binding Sites List in 2p46
Zinc binding site 3 out of 13 in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:29.5
occ:1.00
 NE2 A:HIS105 2.0 22.3 1.0
O A:HOH206 2.0 14.5 1.0
O A:HOH207 2.1 35.5 1.0
CE1 A:HIS105 2.8 26.6 1.0
CD2 A:HIS105 3.1 21.4 1.0
ND1 A:HIS105 4.0 27.5 1.0
CG A:HIS105 4.1 24.6 1.0
CG2 A:THR78 4.2 25.2 1.0
O A:HOH222 4.4 32.1 1.0

Zinc binding site 4 out of 13 in 2p46

Go back to Zinc Binding Sites List in 2p46
Zinc binding site 4 out of 13 in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:28.6
occ:0.35
 OE2 A:GLU49 2.0 27.3 1.0
O A:HOH209 2.1 21.5 1.0
O A:HOH208 2.4 19.5 1.0
OE1 A:GLU49 2.5 31.0 1.0
CD A:GLU49 2.5 29.8 1.0
CG A:GLU49 4.0 29.0 1.0
OG A:SER80 4.1 30.2 1.0
O A:HIS48 4.7 30.5 1.0
O A:HOH220 4.7 22.2 1.0
ZN A:ZN204 4.7 29.9 0.2
N A:SER80 4.8 28.8 1.0
CB A:GLU49 5.0 28.8 1.0

Zinc binding site 5 out of 13 in 2p46

Go back to Zinc Binding Sites List in 2p46
Zinc binding site 5 out of 13 in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:29.9
occ:0.25
 OD2 A:ASP53 1.8 34.0 1.0
CG A:ASP53 3.0 29.3 1.0
OE1 A:GLU49 3.3 31.0 1.0
OD1 A:ASP53 3.7 30.8 1.0
OG A:SER50 4.0 28.0 1.0
CB A:ASP53 4.0 27.4 1.0
N A:SER50 4.1 28.7 1.0
CB A:SER50 4.4 28.0 1.0
CD A:GLU49 4.5 29.8 1.0
O A:HOH215 4.6 24.1 1.0
CB A:GLU49 4.7 28.8 1.0
ZN A:ZN203 4.7 28.6 0.3
CA A:GLU49 4.9 29.0 1.0
CA A:SER50 4.9 28.1 1.0
C A:GLU49 5.0 28.6 1.0

Zinc binding site 6 out of 13 in 2p46

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Zinc binding site 6 out of 13 in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:32.2
occ:0.35
 OD1 A:ASP121 1.7 33.1 1.0
NE2 A:HIS119 2.0 33.0 1.0
O A:HOH210 2.3 21.8 1.0
O A:HOH211 2.5 52.7 1.0
CE1 A:HIS119 2.7 31.3 1.0
CG A:ASP121 2.9 32.2 1.0
CD2 A:HIS119 3.2 31.5 1.0
OD2 A:ASP121 3.8 34.3 1.0
CB A:ASP121 3.8 29.9 1.0
ND1 A:HIS119 3.9 30.4 1.0
CA A:ASP121 3.9 29.5 1.0
CB A:LYS66 4.1 27.7 1.0
CG A:HIS119 4.1 30.6 1.0
N A:LYS66 4.3 27.3 1.0
N A:ASN67 4.5 27.1 1.0
CA A:LYS66 4.7 27.4 1.0
O A:PHE120 4.8 28.8 1.0
CG A:LYS66 4.8 28.2 1.0
O A:ASP121 4.8 30.2 1.0
N A:ASP121 4.8 29.2 1.0
C A:ASP121 4.9 29.9 1.0
CD A:LYS66 4.9 29.7 1.0
C A:LYS66 5.0 27.0 1.0

Zinc binding site 7 out of 13 in 2p46

Go back to Zinc Binding Sites List in 2p46
Zinc binding site 7 out of 13 in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn206

b:32.9
occ:0.25
 OD2 B:ASP105 3.0 42.6 1.0
CG B:ASP105 3.7 37.7 1.0
O B:LEU103 3.7 30.0 1.0
OD1 B:ASP105 3.9 41.2 1.0
N B:GLY47 4.1 32.2 1.0
O B:ARG45 4.2 36.0 1.0
CA B:GLU46 4.5 34.8 1.0
N B:ASP105 4.7 32.9 1.0
C B:GLU46 4.7 33.4 1.0
CB B:ASP105 4.8 34.7 1.0
CE2 B:PHE37 4.8 31.1 1.0
CA B:GLY47 4.9 32.8 1.0
C B:LEU103 5.0 30.8 1.0

Zinc binding site 8 out of 13 in 2p46

Go back to Zinc Binding Sites List in 2p46
Zinc binding site 8 out of 13 in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn207

b:30.6
occ:0.50
 ZN C:ZN207 0.0 30.6 0.5
NE2 C:HIS12 2.0 34.8 1.0
CE1 C:HIS12 2.8 33.2 1.0
CD2 C:HIS12 3.2 34.8 1.0
ZN C:ZN207 3.4 41.5 0.5
NZ C:LYS41 3.9 34.4 0.5
OE1 C:GLN11 3.9 42.9 1.0
ND1 C:HIS12 4.0 33.8 1.0
N C:PHE120 4.1 29.7 1.0
CB C:PHE120 4.2 28.8 1.0
CG C:HIS12 4.2 34.1 1.0
CD C:GLN11 4.3 36.1 1.0
O C:PHE120 4.4 30.0 1.0
CB C:GLN11 4.6 34.7 1.0
CA C:PHE120 4.6 29.4 1.0
NE2 C:GLN11 4.7 37.7 1.0
OD1 C:ASN44 4.8 33.3 1.0
CG C:GLN11 4.9 35.7 1.0
ND1 C:HIS119 4.9 33.5 1.0

Zinc binding site 9 out of 13 in 2p46

Go back to Zinc Binding Sites List in 2p46
Zinc binding site 9 out of 13 in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn207

b:41.5
occ:0.50
 ZN C:ZN207 0.0 41.5 0.5
ND1 C:HIS119 2.2 33.5 1.0
CE1 C:HIS119 3.0 35.0 1.0
CG C:HIS119 3.2 32.9 1.0
ZN C:ZN207 3.4 30.6 0.5
CB C:HIS119 3.5 30.6 1.0
CA C:HIS119 3.8 29.9 1.0
N C:PHE120 4.0 29.7 1.0
NE2 C:HIS119 4.2 35.2 1.0
CD2 C:HIS119 4.3 35.7 1.0
C C:HIS119 4.3 30.0 1.0
O C:PHE120 4.4 30.0 1.0
O C:VAL118 4.8 29.0 1.0
C C:PHE120 5.0 29.4 1.0

Zinc binding site 10 out of 13 in 2p46

Go back to Zinc Binding Sites List in 2p46
Zinc binding site 10 out of 13 in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 2.5A Resolution: SE5B-Ortho-2 Crystal Form with Five Se-Met Sites (L4M, M34, M51, F68M, M83) in Vhh Scaffold. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn208

b:32.4
occ:1.00
 NE2 C:HIS105 1.9 26.2 1.0
O C:HOH212 2.1 27.6 1.0
O C:HOH211 2.2 34.8 1.0
CE1 C:HIS105 2.8 27.1 1.0
CD2 C:HIS105 3.1 25.9 1.0
ND1 C:HIS105 4.0 28.4 1.0
CG C:HIS105 4.1 28.1 1.0
CG2 C:THR78 4.3 29.6 1.0
O C:HOH225 4.3 30.7 1.0

Reference:

V.Tereshko, S.Uysal, A.Koide, K.Margalef, S.Koide, A.A.Kossiakoff. Toward Chaperone-Assisted Crystallography: Protein Engineering Enhancement of Crystal Packing and X-Ray Phasing Capabilities of A Camelid Single-Domain Antibody (Vhh) Scaffold Protein Sci. V. 17 1175 2008.
ISSN: ISSN 0961-8368
PubMed: 18445622
DOI: 10.1110/PS.034892.108
Page generated: Thu Oct 17 02:55:50 2024

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