Chlorine in PDB 7kf1: Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf

Protein crystallography data

The structure of Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf, PDB code: 7kf1 was solved by R.Shi, M.-E.Picard, M.S.Manenda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.57 / 2.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 194.167, 100.749, 153.509, 90, 91.69, 90
R / Rfree (%) 18.9 / 23.2

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf (pdb code 7kf1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf, PDB code: 7kf1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 7kf1

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Chlorine binding site 1 out of 12 in the Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl301

b:22.8
occ:1.00
 O H:HOH450 3.0 17.5 1.0
O H:HOH468 3.2 25.6 1.0
N H:TRP47 3.3 19.4 1.0
N L:PHE98 3.4 21.9 1.0
CA L:THR97 3.8 26.1 1.0
CB H:TRP47 3.9 19.4 1.0
CB L:THR97 3.9 26.0 1.0
CA H:GLU46 4.0 19.7 1.0
CG2 L:THR97 4.0 28.3 1.0
CD2 L:PHE98 4.1 20.0 1.0
C H:GLU46 4.1 19.3 1.0
C L:THR97 4.1 25.2 1.0
CA H:TRP47 4.2 19.9 1.0
CB L:PHE98 4.2 20.1 1.0
O H:LEU45 4.3 18.7 1.0
CA L:PHE98 4.3 19.8 1.0
O L:PHE98 4.4 17.7 1.0
O H:TRP47 4.5 20.2 1.0
CG L:PHE98 4.6 18.8 1.0
CG H:GLU46 4.6 22.5 1.0
O H:HOH416 4.8 20.6 1.0
CB H:GLU46 4.8 21.1 1.0
C L:PHE98 4.9 18.6 1.0
N H:GLU46 4.9 19.0 1.0
O L:PRO96 4.9 48.2 1.0
C H:TRP47 4.9 19.9 1.0
C H:LEU45 4.9 20.0 1.0

Chlorine binding site 2 out of 12 in 7kf1

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Chlorine binding site 2 out of 12 in the Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl302

b:31.1
occ:1.00
 N H:TYR59 3.3 20.7 1.0
O H:HOH518 3.6 40.9 1.0
NE H:ARG58 3.6 45.8 1.0
CA H:ARG58 3.6 24.9 1.0
NZ H:LYS64 3.6 48.3 1.0
CD H:LYS64 3.8 45.3 1.0
O H:TYR59 3.9 23.6 1.0
C H:ARG58 3.9 23.1 1.0
CD H:ARG58 4.0 37.7 1.0
CD2 H:TYR59 4.2 18.6 1.0
CE H:LYS64 4.2 50.7 1.0
CB H:ARG58 4.2 28.6 1.0
CA H:TYR59 4.2 22.6 1.0
O H:HOH484 4.3 43.0 1.0
CB H:TYR59 4.4 20.8 1.0
O H:THR57 4.5 19.5 1.0
C H:TYR59 4.5 23.0 1.0
O H:HOH413 4.6 19.9 1.0
CZ H:ARG58 4.7 48.5 1.0
CG H:ARG58 4.7 34.3 1.0
N H:ARG58 4.8 24.6 1.0
CG H:TYR59 4.8 20.0 1.0
NH1 H:ARG58 4.8 45.8 1.0
C H:THR57 5.0 22.5 1.0

Chlorine binding site 3 out of 12 in 7kf1

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Chlorine binding site 3 out of 12 in the Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl303

b:34.3
occ:1.00
 NH1 H:ARG50 3.0 31.6 1.0
OH H:TYR100A 3.3 45.4 1.0
O L:HOH459 3.3 28.5 1.0
CE1 H:HIS35 3.3 22.4 1.0
NE2 H:HIS35 3.4 20.8 1.0
CD H:ARG50 3.4 29.5 1.0
CG2 L:THR94 3.7 26.1 1.0
CB L:THR94 3.8 29.0 1.0
CD L:PRO96 3.8 33.6 1.0
CE2 H:TYR100A 3.9 40.0 1.0
CZ H:ARG50 4.0 33.2 1.0
CG L:PRO96 4.1 34.0 1.0
CZ H:TYR100A 4.1 39.8 1.0
NE H:ARG50 4.2 29.7 1.0
OG1 L:THR94 4.2 23.1 1.0
CD1 H:LEU95 4.3 39.3 1.0
CG H:TYR33 4.6 26.4 1.0
CD2 H:TYR33 4.6 27.1 1.0
CG H:ARG50 4.6 28.5 1.0
ND1 H:HIS35 4.6 21.6 1.0
N L:PRO96 4.8 33.6 1.0
CD2 H:HIS35 4.8 22.7 1.0
CE2 H:TYR33 4.8 31.1 1.0
CD1 H:TYR33 4.9 28.4 1.0
CA L:PRO95 4.9 36.7 1.0
CB L:PRO96 4.9 34.1 1.0
CB H:TYR33 5.0 23.3 1.0

Chlorine binding site 4 out of 12 in 7kf1

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Chlorine binding site 4 out of 12 in the Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl301

b:42.9
occ:1.00
 N L:VAL115 3.1 23.4 1.0
O L:HOH464 3.2 37.8 1.0
NZ L:LYS207 3.4 45.1 1.0
CA L:SER114 3.7 27.0 1.0
C L:SER114 3.9 24.9 1.0
O L:VAL115 4.0 29.3 1.0
CA L:VAL115 4.1 22.5 1.0
CB L:VAL115 4.2 23.7 1.0
CG2 L:VAL115 4.3 24.2 1.0
O L:PRO113 4.3 23.3 1.0
CB L:SER114 4.3 29.7 1.0
CG1 L:VAL205 4.4 36.1 1.0
CE L:LYS207 4.5 43.0 1.0
C L:VAL115 4.5 25.9 1.0
N L:SER114 4.8 25.6 1.0
C L:PRO113 5.0 23.8 1.0

Chlorine binding site 5 out of 12 in 7kf1

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Chlorine binding site 5 out of 12 in the Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:34.4
occ:1.00
 O A:HOH423 3.3 28.0 1.0
N A:TRP47 3.3 33.5 1.0
N B:PHE98 3.3 34.5 1.0
CA B:THR97 3.6 40.0 1.0
CB B:THR97 3.8 40.5 1.0
CB A:TRP47 3.9 35.6 1.0
CG2 B:THR97 4.0 42.3 1.0
CA A:GLU46 4.0 32.9 1.0
CD2 B:PHE98 4.0 42.6 1.0
C B:THR97 4.0 36.5 1.0
C A:GLU46 4.1 31.5 1.0
CA A:TRP47 4.2 32.6 1.0
CB B:PHE98 4.2 35.2 1.0
O A:LEU45 4.3 32.0 1.0
CA B:PHE98 4.3 34.7 1.0
O B:PHE98 4.4 37.5 1.0
CG B:PHE98 4.6 37.3 1.0
O A:TRP47 4.6 35.4 1.0
CG A:GLU46 4.7 36.7 1.0
O B:PRO96 4.7 57.2 1.0
CB A:GLU46 4.9 32.8 1.0
N B:THR97 4.9 42.6 1.0
C B:PHE98 4.9 33.8 1.0
N A:GLU46 4.9 35.5 1.0
C A:TRP47 4.9 34.5 1.0
C A:LEU45 4.9 33.6 1.0
CE2 B:PHE98 5.0 43.7 1.0

Chlorine binding site 6 out of 12 in 7kf1

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Chlorine binding site 6 out of 12 in the Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:55.7
occ:1.00
 OH A:TYR100A 2.9 60.3 1.0
NH1 A:ARG50 3.0 53.1 1.0
CE1 A:HIS35 3.4 41.7 1.0
NE2 A:HIS35 3.4 42.5 1.0
CD A:ARG50 3.6 48.8 1.0
CE2 A:TYR100A 3.6 59.5 1.0
O B:HOH362 3.6 44.1 1.0
CG2 B:THR94 3.7 53.8 1.0
CZ A:TYR100A 3.7 60.5 1.0
CB B:THR94 3.8 53.9 1.0
CD B:PRO96 3.9 54.3 1.0
CZ A:ARG50 4.0 53.8 1.0
CG B:PRO96 4.1 55.9 1.0
NE A:ARG50 4.2 50.5 1.0
OG1 B:THR94 4.2 47.1 1.0
CD1 A:LEU95 4.2 62.5 1.0
CG A:TYR33 4.6 42.7 1.0
ND1 A:HIS35 4.7 38.6 1.0
CD1 A:TYR33 4.7 46.0 1.0
CD2 A:TYR33 4.7 47.5 1.0
CG A:ARG50 4.7 46.9 1.0
CD2 A:HIS35 4.8 41.4 1.0
N B:PRO96 4.9 51.8 1.0
CE1 A:TYR33 4.9 53.2 1.0
CD2 A:TYR100A 4.9 57.2 1.0
CB B:PRO96 4.9 53.3 1.0
CE2 A:TYR33 4.9 48.6 1.0
CB A:TYR33 5.0 43.6 1.0

Chlorine binding site 7 out of 12 in 7kf1

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Chlorine binding site 7 out of 12 in the Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:54.2
occ:1.00
 N A:TYR59 3.4 42.0 1.0
CE A:LYS64 3.5 67.7 1.0
NZ A:LYS64 3.5 67.9 1.0
CA A:ARG58 3.7 42.9 1.0
NE A:ARG58 3.7 52.6 1.0
O A:TYR59 4.0 36.5 1.0
CD A:ARG58 4.0 49.7 1.0
C A:ARG58 4.0 38.8 1.0
CD1 A:TYR59 4.1 43.6 1.0
CB A:ARG58 4.3 45.4 1.0
CA A:TYR59 4.3 45.1 1.0
CB A:TYR59 4.4 45.8 1.0
O A:HOH409 4.5 42.4 1.0
O A:THR57 4.5 46.7 1.0
C A:TYR59 4.6 41.6 1.0
CD A:LYS64 4.7 64.8 1.0
CG A:ARG58 4.7 49.8 1.0
CG A:TYR59 4.8 46.7 1.0
N A:ARG58 4.8 49.0 1.0
CZ A:ARG58 4.9 54.3 1.0
CG A:LYS64 5.0 59.2 1.0

Chlorine binding site 8 out of 12 in 7kf1

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Chlorine binding site 8 out of 12 in the Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:30.7
occ:1.00
 O D:HOH425 3.1 27.9 1.0
N D:TRP47 3.3 26.1 1.0
N E:PHE98 3.3 31.5 1.0
CA E:THR97 3.7 35.4 1.0
CB D:TRP47 3.9 26.4 1.0
CD2 E:PHE98 3.9 33.1 1.0
CB E:THR97 3.9 34.8 1.0
CA D:GLU46 3.9 27.9 1.0
C E:THR97 4.0 33.7 1.0
CG2 E:THR97 4.0 35.1 1.0
C D:GLU46 4.1 27.8 1.0
CB E:PHE98 4.1 28.5 1.0
CA D:TRP47 4.1 27.8 1.0
O D:LEU45 4.2 29.0 1.0
CA E:PHE98 4.3 28.7 1.0
O E:PHE98 4.4 26.3 1.0
CG E:PHE98 4.5 28.7 1.0
O D:TRP47 4.7 28.0 1.0
O E:PRO96 4.7 43.7 1.0
CG D:GLU46 4.8 34.0 1.0
N D:GLU46 4.8 27.9 1.0
C E:PHE98 4.8 27.4 1.0
CB D:GLU46 4.9 29.6 1.0
C D:LEU45 4.9 27.5 1.0
CE2 E:PHE98 4.9 31.2 1.0
N E:THR97 4.9 34.8 1.0
C D:TRP47 5.0 30.7 1.0
O D:HOH430 5.0 32.6 1.0

Chlorine binding site 9 out of 12 in 7kf1

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Chlorine binding site 9 out of 12 in the Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:42.6
occ:1.00
 N D:TYR59 3.4 31.7 1.0
NH1 D:ARG58 3.4 55.7 1.0
NZ D:LYS64 3.5 58.1 1.0
CA D:ARG58 3.7 32.3 1.0
CE D:LYS64 3.7 53.0 1.0
O D:HOH501 3.7 45.5 1.0
CD D:ARG58 3.8 40.6 1.0
O D:TYR59 3.9 30.9 1.0
C D:ARG58 4.0 29.7 1.0
O D:HOH507 4.0 45.7 1.0
CD D:LYS64 4.2 48.0 1.0
CD1 D:TYR59 4.2 28.9 1.0
CB D:ARG58 4.2 34.1 1.0
CZ D:ARG58 4.3 50.5 1.0
CA D:TYR59 4.3 31.9 1.0
O D:HOH434 4.4 29.1 1.0
O D:THR57 4.4 28.9 1.0
NE D:ARG58 4.4 48.6 1.0
CB D:TYR59 4.5 32.8 1.0
C D:TYR59 4.6 32.4 1.0
CG D:ARG58 4.6 35.8 1.0
N D:ARG58 4.8 33.2 1.0
CG D:TYR59 4.9 32.5 1.0
CG D:LYS64 5.0 41.0 1.0
C D:THR57 5.0 33.8 1.0

Chlorine binding site 10 out of 12 in 7kf1

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Chlorine binding site 10 out of 12 in the Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of BH1 Fab Variant (Cdr H3 Loop Design 14_0130) in Complex with Vegf within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl303

b:46.2
occ:1.00
 NH1 D:ARG50 3.1 37.1 1.0
OH D:TYR100A 3.2 42.3 1.0
O E:HOH365 3.2 30.8 1.0
NE2 D:HIS35 3.4 27.5 1.0
CE1 D:HIS35 3.4 29.0 1.0
CD D:ARG50 3.4 31.2 1.0
CE2 D:TYR100A 3.7 45.3 1.0
CZ D:TYR100A 3.9 43.9 1.0
CG2 E:THR94 3.9 37.8 1.0
CB E:THR94 3.9 38.4 1.0
CZ D:ARG50 4.0 35.9 1.0
CD E:PRO96 4.1 41.8 1.0
NE D:ARG50 4.1 30.9 1.0
CG E:PRO96 4.3 40.6 1.0
CD1 D:LEU95 4.3 39.6 1.0
OG1 E:THR94 4.3 33.6 1.0
CD2 D:TYR33 4.4 37.1 1.0
CG D:TYR33 4.4 36.2 1.0
CE2 D:TYR33 4.6 36.1 1.0
CG D:ARG50 4.6 31.1 1.0
CD1 D:TYR33 4.6 37.0 1.0
ND1 D:HIS35 4.7 26.3 1.0
CD2 D:HIS35 4.8 27.8 1.0
CB D:TYR33 4.8 34.4 1.0
CZ D:TYR33 4.8 41.5 1.0
CE1 D:TYR33 4.9 38.9 1.0
CD2 D:TYR100A 4.9 44.0 1.0

Reference:

M.-E.Picard, M.S.Manenda, C.Corbeil, T.Sulea, J.Baardsness, H.Hogues, F.Gaudreault, C.Deprez, E.O.Purisima, R.Shi. Crystal Structure of BH1 Fab Cdr H3 Loop Variants in Apo Form and in Complex with Vegf To Be Published.
Page generated: Mon Jul 29 23:32:16 2024

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