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Calcium in PDB 3cqo: Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum

Protein crystallography data

The structure of Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum, PDB code: 3cqo was solved by M.A.Bianchet, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.15 / 2.32
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.135, 88.135, 230.169, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 24.5

Other elements in 3cqo:

The structure of Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum (pdb code 3cqo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum, PDB code: 3cqo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3cqo

Go back to Calcium Binding Sites List in 3cqo
Calcium binding site 1 out of 6 in the Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4001

b:21.4
occ:1.00
 OE1 A:GLU140 2.2 22.0 1.0
O A:CYS139 2.3 19.8 1.0
O A:ASN32 2.4 22.5 1.0
O A:SER41 2.4 20.1 1.0
O A:ASN27 2.4 19.2 1.0
OD1 A:ASP30 2.5 23.2 1.0
OG A:SER41 2.5 16.2 1.0
CG A:ASP30 3.4 24.7 1.0
CD A:GLU140 3.4 21.2 1.0
C A:CYS139 3.5 18.8 1.0
C A:SER41 3.5 19.1 1.0
C A:ASN32 3.5 23.4 1.0
CB A:SER41 3.6 17.1 1.0
C A:ASN27 3.6 19.9 1.0
OD2 A:ASP30 3.8 23.3 1.0
CA A:SER41 4.0 18.8 1.0
N A:ASN32 4.1 24.1 1.0
CB A:GLU140 4.1 16.7 1.0
CA A:ASN32 4.2 23.7 1.0
CB A:ASN32 4.2 24.3 1.0
CA A:GLU140 4.2 17.9 1.0
CA A:ALA28 4.3 19.4 1.0
N A:GLU140 4.3 18.3 1.0
OE2 A:GLU140 4.3 22.6 1.0
CG A:GLU140 4.3 18.1 1.0
N A:ALA28 4.4 19.3 1.0
CA A:CYS139 4.5 20.3 1.0
C A:ALA28 4.5 19.7 1.0
CA A:ASN27 4.6 20.0 1.0
N A:ARG33 4.6 23.9 1.0
N A:CYS42 4.6 19.7 1.0
N A:ASP30 4.6 19.3 1.0
CB A:ASP30 4.7 20.8 1.0
O A:ALA28 4.8 19.1 1.0
CB A:ASN27 4.9 19.3 1.0
CA A:ARG33 4.9 24.8 1.0
N A:ILE29 5.0 18.7 1.0
N A:GLY31 5.0 19.4 1.0

Calcium binding site 2 out of 6 in 3cqo

Go back to Calcium Binding Sites List in 3cqo
Calcium binding site 2 out of 6 in the Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4004

b:24.4
occ:1.00
 O A:CYS283 2.3 26.3 1.0
OD1 A:ASP176 2.3 25.7 1.0
O A:ASN178 2.4 20.6 1.0
O A:ASN173 2.4 21.8 1.0
OE1 A:GLU284 2.4 20.7 1.0
OG A:SER187 2.4 20.4 1.0
O A:SER187 2.5 25.6 1.0
CG A:ASP176 3.3 24.6 1.0
C A:CYS283 3.5 25.4 1.0
C A:ASN178 3.5 23.4 1.0
OD2 A:ASP176 3.5 23.2 1.0
CB A:SER187 3.5 21.8 1.0
C A:SER187 3.6 24.6 1.0
C A:ASN173 3.6 20.6 1.0
CD A:GLU284 3.7 23.6 1.0
CA A:SER187 4.1 23.9 1.0
N A:ASN178 4.2 23.3 1.0
CB A:GLU284 4.2 22.5 1.0
CA A:ASN178 4.2 22.9 1.0
CB A:ASN178 4.3 23.2 1.0
CA A:GLU284 4.3 23.3 1.0
N A:GLU284 4.3 24.3 1.0
CA A:ALA174 4.4 20.7 1.0
CA A:CYS283 4.4 26.0 1.0
N A:ALA174 4.5 21.1 1.0
CG A:GLU284 4.5 20.7 1.0
OE2 A:GLU284 4.5 22.8 1.0
CA A:ASN173 4.6 19.3 1.0
N A:ASP176 4.6 22.9 1.0
CB A:ASP176 4.6 23.7 1.0
N A:GLN179 4.6 24.6 1.0
C A:ALA174 4.6 21.2 1.0
N A:CYS188 4.8 26.1 1.0
CA A:GLN179 4.9 25.5 1.0
CB A:ASN173 4.9 17.4 1.0
N A:ILE175 5.0 21.1 1.0
O A:ALA174 5.0 21.6 1.0

Calcium binding site 3 out of 6 in 3cqo

Go back to Calcium Binding Sites List in 3cqo
Calcium binding site 3 out of 6 in the Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4002

b:21.0
occ:1.00
 O B:CYS139 2.2 24.1 1.0
O B:ASN32 2.3 26.1 1.0
OE1 B:GLU140 2.4 19.4 1.0
O B:ASN27 2.4 21.2 1.0
OG B:SER41 2.4 21.8 1.0
O B:SER41 2.5 21.5 1.0
OD1 B:ASP30 2.5 17.4 1.0
CG B:ASP30 3.4 19.8 1.0
C B:CYS139 3.4 23.9 1.0
C B:ASN32 3.5 23.9 1.0
CD B:GLU140 3.5 21.6 1.0
C B:SER41 3.5 22.2 1.0
CB B:SER41 3.6 20.6 1.0
C B:ASN27 3.6 19.7 1.0
OD2 B:ASP30 3.7 21.3 1.0
CB B:GLU140 3.9 22.5 1.0
CA B:SER41 4.0 21.3 1.0
CA B:GLU140 4.1 21.7 1.0
N B:ASN32 4.1 19.1 1.0
N B:GLU140 4.2 22.1 1.0
CA B:ASN32 4.3 21.0 1.0
CG B:GLU140 4.3 20.5 1.0
CA B:ALA28 4.3 20.1 1.0
CB B:ASN32 4.4 21.8 1.0
N B:ALA28 4.4 20.4 1.0
OE2 B:GLU140 4.4 21.1 1.0
CA B:CYS139 4.5 25.3 1.0
N B:ARG33 4.5 25.2 1.0
C B:ALA28 4.5 19.5 1.0
CA B:ASN27 4.6 19.7 1.0
CB B:ASP30 4.7 17.3 1.0
N B:ASP30 4.7 16.4 1.0
N B:CYS42 4.7 22.0 1.0
CA B:ARG33 4.7 24.8 1.0
CB B:ASN27 4.8 18.1 1.0
O B:ALA28 4.8 19.1 1.0

Calcium binding site 4 out of 6 in 3cqo

Go back to Calcium Binding Sites List in 3cqo
Calcium binding site 4 out of 6 in the Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4006

b:27.5
occ:1.00
 OG B:SER187 2.1 24.3 1.0
O B:CYS283 2.3 27.0 1.0
OD1 B:ASP176 2.4 24.9 1.0
O B:ASN173 2.4 23.6 1.0
O B:ASN178 2.4 29.2 1.0
OE1 B:GLU284 2.5 22.5 1.0
O B:SER187 2.5 30.5 1.0
CG B:ASP176 3.3 24.7 1.0
CB B:SER187 3.4 28.1 1.0
OD2 B:ASP176 3.5 26.3 1.0
C B:SER187 3.5 30.0 1.0
C B:CYS283 3.5 27.3 1.0
C B:ASN173 3.6 24.0 1.0
C B:ASN178 3.6 28.0 1.0
CD B:GLU284 3.7 23.2 1.0
CA B:SER187 3.9 28.7 1.0
N B:ASN178 4.2 26.5 1.0
CB B:GLU284 4.2 25.2 1.0
CA B:ASN178 4.2 26.7 1.0
CB B:ASN178 4.3 25.9 1.0
CA B:ALA174 4.3 23.5 1.0
CA B:GLU284 4.4 24.8 1.0
N B:GLU284 4.4 25.3 1.0
N B:ALA174 4.4 24.4 1.0
CA B:CYS283 4.5 29.2 1.0
CG B:GLU284 4.5 22.8 1.0
CA B:ASN173 4.5 24.0 1.0
OE2 B:GLU284 4.6 23.1 1.0
CB B:ASP176 4.6 21.1 1.0
C B:ALA174 4.6 22.7 1.0
N B:GLN179 4.7 29.5 1.0
N B:ASP176 4.7 20.0 1.0
N B:CYS188 4.7 29.9 1.0
CB B:ASN173 4.8 25.6 1.0
O B:ALA174 4.9 22.5 1.0
CG B:ASN178 4.9 24.6 1.0
CA B:GLN179 4.9 30.7 1.0

Calcium binding site 5 out of 6 in 3cqo

Go back to Calcium Binding Sites List in 3cqo
Calcium binding site 5 out of 6 in the Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4003

b:17.1
occ:1.00
 OE1 C:GLU140 2.3 19.7 1.0
O C:ASN27 2.3 17.3 1.0
OD1 C:ASP30 2.4 26.7 1.0
O C:SER41 2.4 18.6 1.0
O C:ASN32 2.4 22.1 1.0
O C:CYS139 2.4 21.7 1.0
OG C:SER41 2.6 18.9 1.0
CG C:ASP30 3.3 25.0 1.0
C C:ASN27 3.5 17.6 1.0
C C:SER41 3.5 18.8 1.0
CD C:GLU140 3.5 19.6 1.0
C C:ASN32 3.6 23.1 1.0
C C:CYS139 3.6 22.1 1.0
CB C:SER41 3.7 18.1 1.0
OD2 C:ASP30 3.7 23.2 1.0
CA C:SER41 4.0 18.7 1.0
N C:ASN32 4.1 21.8 1.0
CB C:GLU140 4.1 20.6 1.0
CA C:ASN32 4.2 22.1 1.0
CB C:ASN32 4.2 21.5 1.0
CA C:GLU140 4.2 22.6 1.0
CA C:ALA28 4.3 18.8 1.0
N C:ALA28 4.3 17.3 1.0
N C:GLU140 4.3 21.9 1.0
OE2 C:GLU140 4.4 20.7 1.0
CG C:GLU140 4.4 18.4 1.0
C C:ALA28 4.5 18.8 1.0
CA C:ASN27 4.5 18.7 1.0
N C:ASP30 4.5 20.8 1.0
CB C:ASP30 4.6 21.0 1.0
CA C:CYS139 4.6 22.9 1.0
N C:CYS42 4.6 19.5 1.0
N C:ARG33 4.7 23.2 1.0
CB C:ASN27 4.7 18.5 1.0
O C:ALA28 4.8 20.2 1.0
N C:ILE29 4.8 18.9 1.0
N C:GLY31 4.9 22.0 1.0
CA C:ASP30 5.0 20.3 1.0
CA C:ARG33 5.0 23.3 1.0

Calcium binding site 6 out of 6 in 3cqo

Go back to Calcium Binding Sites List in 3cqo
Calcium binding site 6 out of 6 in the Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A F-Lectin (Fucolectin) From Morone Saxatilis (Striped Bass) Serum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4005

b:25.5
occ:1.00
 O C:ASN173 2.3 24.0 1.0
O C:CYS283 2.3 27.4 1.0
OD1 C:ASP176 2.4 23.6 1.0
O C:ASN178 2.4 25.8 1.0
OE1 C:GLU284 2.4 33.6 1.0
OG C:SER187 2.5 22.1 1.0
O C:SER187 2.5 21.6 1.0
CG C:ASP176 3.4 21.8 1.0
C C:CYS283 3.4 25.4 1.0
CB C:SER187 3.5 22.8 1.0
C C:ASN173 3.5 23.2 1.0
C C:SER187 3.6 22.8 1.0
C C:ASN178 3.6 24.9 1.0
CD C:GLU284 3.6 33.5 1.0
OD2 C:ASP176 3.8 22.1 1.0
CA C:SER187 4.0 22.2 1.0
CB C:GLU284 4.1 27.5 1.0
CA C:GLU284 4.2 25.3 1.0
CA C:ALA174 4.2 22.5 1.0
N C:GLU284 4.2 25.1 1.0
N C:ASN178 4.2 23.4 1.0
N C:ALA174 4.3 23.3 1.0
CA C:ASN178 4.3 23.2 1.0
CG C:GLU284 4.4 30.1 1.0
CA C:CYS283 4.4 25.2 1.0
C C:ALA174 4.4 23.6 1.0
CB C:ASN178 4.5 23.3 1.0
CA C:ASN173 4.5 23.8 1.0
OE2 C:GLU284 4.6 34.1 1.0
N C:ASP176 4.6 22.8 1.0
CB C:ASP176 4.6 21.3 1.0
N C:GLN179 4.7 25.5 1.0
O C:ALA174 4.7 25.0 1.0
CB C:ASN173 4.7 22.2 1.0
N C:CYS188 4.8 22.7 1.0
CA C:GLN179 4.9 25.4 1.0
N C:ILE175 4.9 24.9 1.0

Reference:

M.A.Bianchet, E.W.Odom, G.R.Vasta, L.M.Amzel. Structure and Specificity of A Binary Tandem Domain F-Lectin From Striped Bass (Morone Saxatilis). J.Mol.Biol. V. 401 239 2010.
ISSN: ISSN 0022-2836
PubMed: 20561530
DOI: 10.1016/J.JMB.2010.06.018
Page generated: Sat Jul 13 08:44:18 2024

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