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Chlorine in PDB 5c6w: Anti-CXCL13 Scfv - E10

Protein crystallography data

The structure of Anti-CXCL13 Scfv - E10, PDB code: 5c6w was solved by C.Tu, J.Bard, L.Mosyak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.980, 80.360, 119.240, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 16.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Anti-CXCL13 Scfv - E10 (pdb code 5c6w). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Anti-CXCL13 Scfv - E10, PDB code: 5c6w:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5c6w

Go back to Chlorine Binding Sites List in 5c6w
Chlorine binding site 1 out of 6 in the Anti-CXCL13 Scfv - E10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Anti-CXCL13 Scfv - E10 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1201

b:85.7
occ:1.00
 O H:HOH1455 3.5 58.0 1.0
O H:VAL1060 3.8 26.6 1.0
C H:VAL1060 3.8 26.3 1.0
CA H:SER1061 3.9 27.3 0.5
N H:SER1061 3.9 26.1 1.0
CA H:SER1061 4.0 26.1 0.5
C H:GLY1059 4.0 31.4 1.0
O H:GLY1059 4.0 32.3 1.0
N H:VAL1060 4.3 24.6 1.0
CA H:GLY1059 4.3 29.8 1.0
O H:HOH1475 4.4 50.2 1.0
O H:HOH1502 4.5 81.0 1.0
CB H:SER1061 4.5 32.8 0.5
O H:HOH1379 4.5 40.8 1.0
N H:GLY1059 4.6 30.5 1.0
CA H:VAL1060 4.7 21.9 1.0
CB H:SER1061 4.8 27.3 0.5

Chlorine binding site 2 out of 6 in 5c6w

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Chlorine binding site 2 out of 6 in the Anti-CXCL13 Scfv - E10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Anti-CXCL13 Scfv - E10 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1202

b:95.3
occ:1.00
 O1 H:EDO1208 2.9 61.5 1.0
NZ H:LYS23 3.1 58.8 1.0
O H:HOH1406 3.7 43.8 1.0
C1 H:EDO1208 3.9 60.0 1.0
O H:ALA24 3.9 33.5 1.0
CA H:SER25 4.1 24.9 1.0
CB H:SER25 4.2 29.6 1.0
CE H:LYS23 4.4 52.5 1.0
O H:HOH1399 4.4 45.7 1.0
C2 H:EDO1208 4.7 59.1 1.0
N H:GLY26 4.8 25.2 1.0
CB H:SER77 4.8 25.6 1.0
C H:ALA24 4.9 29.8 1.0
O H:HOH1326 4.9 44.2 1.0

Chlorine binding site 3 out of 6 in 5c6w

Go back to Chlorine Binding Sites List in 5c6w
Chlorine binding site 3 out of 6 in the Anti-CXCL13 Scfv - E10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Anti-CXCL13 Scfv - E10 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1203

b:59.8
occ:1.00
 N H:GLY8 3.1 22.2 1.0
CA H:SER7 3.9 19.7 1.0
CA H:GLY8 3.9 21.3 1.0
CB H:SER7 4.0 21.3 1.0
C H:SER7 4.0 22.8 1.0
O H:HOH1539 4.3 55.6 1.0
O H:HOH1442 4.4 43.8 1.0

Chlorine binding site 4 out of 6 in 5c6w

Go back to Chlorine Binding Sites List in 5c6w
Chlorine binding site 4 out of 6 in the Anti-CXCL13 Scfv - E10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Anti-CXCL13 Scfv - E10 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1204

b:97.0
occ:1.00
 O2 H:EDO1207 2.9 57.6 1.0
ND1 H:HIS1062 3.4 39.3 1.0
CB H:HIS1062 3.7 31.6 1.0
CG H:HIS1062 4.0 36.2 1.0
NH2 H:ARG1056 4.1 33.8 1.0
C2 H:EDO1207 4.3 51.6 1.0
CE1 H:HIS1062 4.5 38.7 1.0
C1 H:EDO1207 4.7 52.3 1.0
NH1 H:ARG1056 4.8 28.9 1.0
O H:HIS1062 4.9 29.7 1.0
CZ H:ARG1056 4.9 42.0 1.0

Chlorine binding site 5 out of 6 in 5c6w

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Chlorine binding site 5 out of 6 in the Anti-CXCL13 Scfv - E10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Anti-CXCL13 Scfv - E10 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl1201

b:51.4
occ:1.00
 N J:LYS13 3.0 24.5 1.0
O J:HOH1354 3.6 69.7 1.0
O J:HOH1440 3.6 53.9 1.0
CE J:LYS12 3.7 41.0 1.0
CA J:LYS12 3.7 22.6 1.0
OG J:SER16 3.7 30.1 1.0
CB J:LYS13 3.7 28.1 1.0
CG J:LYS13 3.8 46.5 1.0
C J:LYS12 3.8 26.2 1.0
CB J:SER16 3.9 26.4 1.0
CA J:LYS13 4.0 24.3 1.0
NZ J:LYS12 4.1 45.3 1.0
CB J:LYS12 4.2 24.0 1.0
CD J:LYS12 4.2 34.5 1.0
CD J:LYS13 4.3 56.5 1.0
O J:VAL11 4.5 26.2 1.0
O J:LYS13 4.6 25.9 1.0
CE J:LYS13 4.8 71.7 1.0
CG J:LYS12 4.8 26.6 1.0
C J:LYS13 4.9 27.5 1.0
N J:LYS12 4.9 22.2 1.0

Chlorine binding site 6 out of 6 in 5c6w

Go back to Chlorine Binding Sites List in 5c6w
Chlorine binding site 6 out of 6 in the Anti-CXCL13 Scfv - E10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Anti-CXCL13 Scfv - E10 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl1202

b:84.4
occ:1.00
 ND2 J:ASN1054 3.7 33.4 1.0
O J:HOH1529 3.8 60.5 1.0
O J:HOH1356 3.9 40.6 1.0
OD1 J:ASN1054 4.2 23.7 1.0
O J:HOH1498 4.2 60.2 1.0
CG J:ASN1054 4.4 26.4 1.0

Reference:

C.Tu, V.Terraube, A.Tam, W.Stochaj, B.Fennell, L.Lin, M.Stahl, E.Lavallie, W.Somers, W.Finlay, L.Mosyak, J.Bard, O.Cunningham. Optimization of A Scfv-Based Biotherapeutic By Cdr Side-Chain Clash Repair To Be Published.
Page generated: Sat Jul 12 00:43:15 2025

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