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Chlorine in PDB 3e05: Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15

Enzymatic activity of Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15

All present enzymatic activity of Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15:
2.1.1.132;

Protein crystallography data

The structure of Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15, PDB code: 3e05 was solved by Y.Patskovsky, U.A.Ramagopal, R.Toro, M.Dickey, S.Hu, M.Maletic, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.710, 83.451, 149.056, 90.00, 95.72, 90.00
R / Rfree (%) 21.6 / 26.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15 (pdb code 3e05). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15, PDB code: 3e05:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3e05

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Chlorine binding site 1 out of 8 in the Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15


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 Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1

b:34.2
occ:1.00
 OG A:SER261 2.9 29.7 1.0
O A:HOH451 3.1 34.9 1.0
N A:SER261 3.3 27.6 1.0
N A:SER259 3.5 34.2 1.0
N A:THR232 3.5 32.9 1.0
CB A:SER261 3.6 31.3 1.0
CB A:SER259 3.6 35.4 1.0
CG1 A:ILE231 3.7 37.1 1.0
O A:ALA257 3.7 29.1 1.0
N A:ALA260 3.8 27.4 1.0
CA A:ILE231 3.8 34.9 1.0
CA A:SER259 3.9 36.3 1.0
O A:HOH427 3.9 28.9 1.0
C A:SER259 4.0 34.0 1.0
CA A:SER261 4.0 28.2 1.0
O A:HOH452 4.0 45.7 1.0
C A:ILE231 4.2 33.2 1.0
OG1 A:THR232 4.3 28.7 1.0
C A:ALA260 4.4 28.6 1.0
CB A:ILE231 4.4 36.4 1.0
O A:LEU230 4.5 33.3 1.0
CB A:THR232 4.5 30.2 1.0
CA A:ALA260 4.5 32.8 1.0
OG A:SER259 4.5 39.7 1.0
CA A:THR232 4.5 30.1 1.0
C A:GLY258 4.6 35.1 1.0
N A:VAL262 4.6 24.8 1.0
N A:ILE231 4.8 32.9 1.0
CA A:GLY258 4.8 34.4 1.0
O A:SER259 4.8 32.6 1.0
C A:ALA257 4.8 29.7 1.0
C A:SER261 4.8 27.3 1.0
CD1 A:ILE231 4.9 36.0 1.0
O A:THR232 5.0 30.6 1.0
C A:LEU230 5.0 37.4 1.0

Chlorine binding site 2 out of 8 in 3e05

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Chlorine binding site 2 out of 8 in the Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15


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 Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1

b:29.0
occ:1.00
 O B:HOH480 3.1 31.9 1.0
OG B:SER261 3.1 26.5 1.0
N B:SER259 3.4 30.5 1.0
N B:SER261 3.4 24.7 1.0
CB B:SER261 3.6 31.7 1.0
N B:THR232 3.6 34.4 1.0
CB B:SER259 3.6 34.5 1.0
N B:ALA260 3.7 27.4 1.0
O B:ALA257 3.8 27.6 1.0
CA B:SER259 3.8 35.1 1.0
CG1 B:ILE231 3.9 35.2 1.0
CA B:ILE231 3.9 32.6 1.0
C B:SER259 3.9 33.8 1.0
CA B:SER261 4.1 28.9 1.0
O B:HOH490 4.2 41.8 1.0
O B:HOH419 4.2 26.8 1.0
OG1 B:THR232 4.3 30.0 1.0
C B:ILE231 4.3 34.3 1.0
C B:ALA260 4.4 28.7 1.0
CB B:THR232 4.5 26.9 1.0
C B:GLY258 4.5 33.9 1.0
CA B:ALA260 4.5 29.6 1.0
CB B:ILE231 4.5 34.5 1.0
O B:LEU230 4.5 31.1 1.0
OG B:SER259 4.6 39.2 1.0
N B:VAL262 4.6 26.5 1.0
CA B:THR232 4.6 30.8 1.0
CA B:GLY258 4.7 26.8 1.0
O B:SER259 4.8 31.5 1.0
C B:ALA257 4.9 27.1 1.0
C B:SER261 4.9 28.4 1.0
N B:ILE231 4.9 34.5 1.0
O B:THR232 5.0 26.4 1.0

Chlorine binding site 3 out of 8 in 3e05

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Chlorine binding site 3 out of 8 in the Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15


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 Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1

b:29.8
occ:1.00
 OG C:SER261 2.9 30.8 1.0
O C:HOH472 3.1 37.8 1.0
N C:SER261 3.4 28.7 1.0
N C:SER259 3.4 27.4 1.0
N C:THR232 3.6 33.7 1.0
CB C:SER259 3.6 33.6 1.0
CB C:SER261 3.7 29.5 1.0
O C:ALA257 3.7 29.1 1.0
CG1 C:ILE231 3.7 33.6 1.0
N C:ALA260 3.7 30.5 1.0
O C:HOH420 3.8 29.0 1.0
CA C:ILE231 3.8 32.7 1.0
CA C:SER259 3.8 31.2 1.0
C C:SER259 4.0 30.3 1.0
O C:HOH454 4.1 38.2 1.0
CA C:SER261 4.1 26.9 1.0
OG1 C:THR232 4.2 29.0 1.0
C C:ILE231 4.2 35.5 1.0
C C:ALA260 4.4 27.4 1.0
CB C:ILE231 4.4 36.6 1.0
CA C:ALA260 4.5 29.2 1.0
CB C:THR232 4.5 29.3 1.0
OG C:SER259 4.5 34.3 1.0
O C:LEU230 4.5 30.0 1.0
C C:GLY258 4.5 32.0 1.0
CA C:THR232 4.6 29.5 1.0
N C:VAL262 4.7 26.7 1.0
CA C:GLY258 4.7 30.0 1.0
N C:ILE231 4.8 32.6 1.0
O C:SER259 4.8 28.1 1.0
C C:ALA257 4.8 27.3 1.0
CD1 C:ILE231 4.9 34.2 1.0
C C:SER261 4.9 25.8 1.0
C C:LEU230 5.0 36.4 1.0
O C:THR232 5.0 27.9 1.0

Chlorine binding site 4 out of 8 in 3e05

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Chlorine binding site 4 out of 8 in the Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15


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 Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1

b:37.5
occ:1.00
 OG D:SER261 3.0 28.9 1.0
O D:HOH458 3.3 34.7 1.0
N D:SER261 3.4 30.4 1.0
N D:SER259 3.4 35.3 1.0
CB D:SER259 3.6 36.8 1.0
CB D:SER261 3.6 31.8 1.0
N D:THR232 3.6 36.5 1.0
N D:ALA260 3.6 33.1 1.0
CG1 D:ILE231 3.7 38.4 1.0
O D:ALA257 3.7 31.2 1.0
CA D:SER259 3.8 35.5 1.0
CA D:ILE231 3.8 37.9 1.0
C D:SER259 3.9 34.7 1.0
CA D:SER261 4.0 29.4 1.0
O D:HOH420 4.0 39.6 1.0
C D:ILE231 4.2 38.0 1.0
O D:HOH472 4.3 45.9 1.0
OG1 D:THR232 4.3 31.1 1.0
C D:ALA260 4.4 28.5 1.0
CB D:ILE231 4.4 35.8 1.0
OG D:SER259 4.4 42.4 1.0
CA D:ALA260 4.4 34.6 1.0
C D:GLY258 4.5 35.8 1.0
CB D:THR232 4.5 31.2 1.0
O D:LEU230 4.6 38.3 1.0
CA D:THR232 4.7 31.1 1.0
N D:VAL262 4.7 22.1 1.0
O D:SER259 4.7 34.4 1.0
CA D:GLY258 4.8 31.0 1.0
N D:ILE231 4.8 37.2 1.0
C D:ALA257 4.8 31.2 1.0
C D:SER261 4.9 27.6 1.0
CD1 D:ILE231 4.9 35.7 1.0

Chlorine binding site 5 out of 8 in 3e05

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Chlorine binding site 5 out of 8 in the Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15


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 Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1

b:38.8
occ:1.00
 OG E:SER261 3.0 34.4 1.0
O E:HOH433 3.3 34.3 1.0
N E:SER259 3.4 38.5 1.0
N E:SER261 3.5 29.9 1.0
CB E:SER259 3.6 38.6 1.0
CB E:SER261 3.6 32.8 1.0
O E:ALA257 3.7 31.4 1.0
N E:ALA260 3.7 32.2 1.0
N E:THR232 3.7 35.4 1.0
CA E:SER259 3.9 37.6 1.0
CA E:ILE231 3.9 37.7 1.0
CG1 E:ILE231 3.9 37.8 1.0
C E:SER259 4.0 35.5 1.0
O E:HOH423 4.1 33.0 1.0
CA E:SER261 4.1 29.9 1.0
O E:HOH456 4.2 41.9 1.0
OG E:SER259 4.2 42.8 1.0
C E:ILE231 4.3 37.1 1.0
OG1 E:THR232 4.4 34.3 1.0
O E:LEU230 4.4 38.3 1.0
C E:ALA260 4.5 29.5 1.0
CB E:ILE231 4.5 38.2 1.0
CA E:ALA260 4.5 32.9 1.0
C E:GLY258 4.5 36.8 1.0
CA E:GLY258 4.7 32.5 1.0
N E:VAL262 4.7 31.2 1.0
CB E:THR232 4.7 33.0 1.0
C E:ALA257 4.8 31.2 1.0
O E:SER259 4.8 37.0 1.0
N E:ILE231 4.8 36.8 1.0
CA E:THR232 4.8 29.5 1.0
C E:LEU230 4.9 40.8 1.0
C E:SER261 5.0 29.4 1.0
CD1 E:ILE231 5.0 37.8 1.0

Chlorine binding site 6 out of 8 in 3e05

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Chlorine binding site 6 out of 8 in the Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15


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 Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl1

b:34.2
occ:1.00
 O F:HOH452 2.9 39.3 1.0
OG F:SER261 3.1 31.6 1.0
N F:SER259 3.3 35.0 1.0
N F:THR232 3.5 32.6 1.0
N F:SER261 3.6 30.6 1.0
O F:ALA257 3.6 31.7 1.0
CB F:SER259 3.7 37.2 1.0
CA F:ILE231 3.7 35.4 1.0
N F:ALA260 3.8 32.8 1.0
O F:HOH460 3.8 36.7 1.0
CB F:SER261 3.8 29.6 1.0
CG1 F:ILE231 3.8 37.0 1.0
CA F:SER259 3.8 33.6 1.0
O F:HOH420 3.9 27.9 1.0
C F:SER259 4.0 31.4 1.0
C F:ILE231 4.1 34.1 1.0
CA F:SER261 4.3 29.4 1.0
OG1 F:THR232 4.3 32.1 1.0
CB F:ILE231 4.3 36.3 1.0
O F:LEU230 4.4 36.6 1.0
C F:GLY258 4.4 35.5 1.0
CB F:THR232 4.5 32.9 1.0
C F:ALA260 4.5 30.7 1.0
CA F:THR232 4.6 30.7 1.0
CA F:ALA260 4.6 33.1 1.0
OG F:SER259 4.6 38.4 1.0
CA F:GLY258 4.6 32.5 1.0
N F:ILE231 4.6 36.2 1.0
C F:ALA257 4.8 27.9 1.0
N F:VAL262 4.8 26.3 1.0
C F:LEU230 4.8 38.9 1.0
O F:SER259 4.9 33.2 1.0
O F:THR232 5.0 32.2 1.0
CD1 F:ILE231 5.0 36.5 1.0

Chlorine binding site 7 out of 8 in 3e05

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Chlorine binding site 7 out of 8 in the Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15


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 Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl1

b:36.0
occ:1.00
 OG G:SER261 2.8 35.1 1.0
N G:SER261 3.4 32.4 1.0
CB G:SER261 3.5 32.3 1.0
CB G:SER259 3.5 37.3 1.0
N G:THR232 3.6 33.7 1.0
N G:SER259 3.6 34.3 1.0
CG1 G:ILE231 3.7 36.5 1.0
N G:ALA260 3.8 33.1 1.0
CA G:ILE231 3.8 35.9 1.0
CA G:SER259 3.9 35.9 1.0
O G:ALA257 3.9 31.8 1.0
O G:HOH462 3.9 38.0 1.0
C G:SER259 4.0 33.8 1.0
O G:HOH427 4.0 42.5 1.0
CA G:SER261 4.0 31.1 1.0
C G:ILE231 4.2 34.7 1.0
OG1 G:THR232 4.2 33.5 1.0
C G:ALA260 4.3 34.3 1.0
OG G:SER259 4.4 43.4 1.0
CB G:ILE231 4.4 36.4 1.0
CA G:ALA260 4.4 34.8 1.0
CB G:THR232 4.4 29.3 1.0
O G:LEU230 4.5 33.6 1.0
N G:VAL262 4.6 29.9 1.0
CA G:THR232 4.6 28.3 1.0
C G:GLY258 4.7 34.4 1.0
O G:SER259 4.7 35.9 1.0
N G:ILE231 4.8 34.1 1.0
C G:SER261 4.8 29.8 1.0
CD1 G:ILE231 4.9 33.4 1.0
CA G:GLY258 5.0 31.4 1.0
C G:LEU230 5.0 37.5 1.0

Chlorine binding site 8 out of 8 in 3e05

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Chlorine binding site 8 out of 8 in the Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15


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 Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens Gs-15 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1

b:48.2
occ:1.00
 OG H:SER261 2.9 33.8 1.0
N H:SER259 3.4 37.3 1.0
O H:HOH444 3.4 41.2 1.0
CB H:SER259 3.5 35.0 1.0
N H:THR232 3.5 37.6 1.0
N H:SER261 3.6 33.4 1.0
CB H:SER261 3.6 35.4 1.0
CG1 H:ILE231 3.6 37.2 1.0
CA H:ILE231 3.7 37.5 1.0
CA H:SER259 3.8 37.1 1.0
N H:ALA260 3.8 32.4 1.0
O H:ALA257 3.9 33.6 1.0
C H:SER259 4.0 36.7 1.0
O H:HOH418 4.1 32.3 1.0
C H:ILE231 4.2 36.3 1.0
CA H:SER261 4.2 31.7 1.0
CB H:ILE231 4.3 36.3 1.0
OG H:SER259 4.3 42.6 1.0
OG1 H:THR232 4.3 35.9 1.0
O H:LEU230 4.4 37.2 1.0
C H:GLY258 4.5 38.1 1.0
C H:ALA260 4.5 31.9 1.0
CB H:THR232 4.6 33.9 1.0
CA H:ALA260 4.6 33.1 1.0
CA H:THR232 4.6 31.9 1.0
CA H:GLY258 4.7 31.8 1.0
N H:ILE231 4.7 38.0 1.0
N H:VAL262 4.7 32.0 1.0
O H:SER259 4.8 39.2 1.0
CD1 H:ILE231 4.8 37.5 1.0
C H:LEU230 4.9 41.0 1.0

Reference:

Y.Patskovsky, U.A.Ramagopal, R.Toro, M.Dickey, S.Hu, M.Maletic, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Precorrin-6Y C5,15-Methyltransferase From Geobacter Metallireducens To Be Published.
Page generated: Sat Jul 20 18:36:16 2024

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