Zinc in PDB 6jf1: Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae

Protein crystallography data

The structure of Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae, PDB code: 6jf1 was solved by B.Jha, R.Vyas, J.Bhushan, D.Sehgal, B.K.Biswal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.91 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.692, 75.851, 75.634, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.1

Other elements in 6jf1:

The structure of Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae (pdb code 6jf1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae, PDB code: 6jf1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 6jf1

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Zinc binding site 1 out of 11 in the Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:20.3
occ:1.00
 NE2 A:HIS-17 1.9 18.8 1.0
NE2 A:HIS-15 1.9 19.5 1.0
OXT A:ACT316 2.0 27.0 1.0
O A:ACT316 2.6 37.0 1.0
C A:ACT316 2.7 30.4 1.0
CE1 A:HIS-15 2.8 20.3 1.0
CE1 A:HIS-17 2.9 20.7 1.0
CD2 A:HIS-17 3.0 21.5 1.0
CD2 A:HIS-15 3.1 18.1 1.0
ND1 A:HIS-15 3.9 19.8 1.0
ND1 A:HIS-17 4.0 21.4 1.0
CG A:HIS-17 4.1 21.1 1.0
CG A:HIS-15 4.1 17.6 1.0
CH3 A:ACT316 4.2 27.3 1.0
CG2 A:THR68 4.4 18.4 1.0
CH3 A:ACT320 5.0 19.9 1.0
O A:HOH504 5.0 37.5 1.0

Zinc binding site 2 out of 11 in 6jf1

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Zinc binding site 2 out of 11 in the Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:25.2
occ:1.00
 O A:HOH500 1.8 29.1 1.0
OE1 A:GLU69 2.0 24.5 1.0
OE1 A:GLU48 2.0 22.1 1.0
OE2 A:GLU69 2.5 25.9 1.0
CD A:GLU69 2.5 23.7 1.0
CD A:GLU48 2.7 24.1 1.0
OE2 A:GLU48 2.7 22.6 1.0
ZN A:ZN304 3.5 27.5 1.0
O A:HOH561 3.5 56.8 1.0
CG A:GLU69 4.0 25.2 1.0
CG A:GLU48 4.1 22.6 1.0
CE1 A:HIS-16 4.2 16.5 1.0
O A:ARG43 4.2 25.3 1.0
NE2 A:HIS-16 4.2 15.9 1.0
CB A:ASN42 4.5 20.5 1.0
CA A:ASN42 4.6 20.9 1.0
N A:ARG43 4.6 20.0 1.0
CB A:GLU69 4.6 20.4 1.0
CB A:GLU48 4.7 23.1 1.0
O A:ACT314 4.8 33.5 1.0
CH3 A:ACT315 5.0 33.5 1.0

Zinc binding site 3 out of 11 in 6jf1

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Zinc binding site 3 out of 11 in the Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:27.5
occ:1.00
 O A:ACT314 1.9 33.5 1.0
O A:HOH500 2.0 29.1 1.0
NE2 A:HIS-16 2.1 15.9 1.0
C A:ACT314 2.8 36.9 0.8
CE1 A:HIS-16 3.0 16.5 1.0
OXT A:ACT314 3.0 39.1 1.0
CD2 A:HIS-16 3.1 15.9 1.0
ZN A:ZN303 3.5 25.2 1.0
ND1 A:HIS-14 3.8 36.0 1.0
O A:HOH561 3.9 56.8 1.0
OE1 A:GLU69 4.0 24.5 1.0
OE2 A:GLU69 4.1 25.9 1.0
ND1 A:HIS-16 4.1 15.8 1.0
CD A:GLU69 4.1 23.7 1.0
CH3 A:ACT314 4.2 31.4 1.0
CG A:HIS-16 4.2 16.6 1.0
CB A:HIS-14 4.3 30.2 1.0
CG A:HIS-14 4.5 37.0 1.0
CE1 A:HIS-14 4.7 33.8 1.0

Zinc binding site 4 out of 11 in 6jf1

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Zinc binding site 4 out of 11 in the Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:41.0
occ:0.85
 O A:HOH444 2.1 38.6 1.0
OXT A:ACT315 2.2 40.2 1.0
O A:HOH562 2.4 38.7 1.0
OD2 A:ASP52 2.4 35.5 1.0
OD1 A:ASP52 2.8 33.2 1.0
CG A:ASP52 2.9 31.8 1.0
ZN A:ZN308 2.9 36.6 0.8
C A:ACT315 3.1 37.1 1.0
O A:HOH540 3.2 33.6 1.0
O A:ACT315 3.3 35.3 1.0
NE2 A:HIS-14 3.9 42.7 1.0
CE1 A:HIS-14 4.2 33.8 1.0
O A:GLU48 4.2 25.7 1.0
CB A:ASP52 4.3 23.4 1.0
CH3 A:ACT315 4.5 33.5 1.0
C A:GLU48 4.7 24.2 1.0
N A:ASP52 4.8 19.7 1.0
O A:HOH455 4.9 40.7 1.0
CB A:GLU48 4.9 23.1 1.0
CE A:LYS49 4.9 49.4 1.0
NE2 A:HIS-12 4.9 41.3 1.0
CD A:LYS49 4.9 40.6 1.0
CD2 A:HIS-14 4.9 38.0 1.0
CA A:LYS49 4.9 25.4 1.0
CA A:ASP52 5.0 22.0 1.0

Zinc binding site 5 out of 11 in 6jf1

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Zinc binding site 5 out of 11 in the Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:38.6
occ:1.00
 O A:HOH413 2.0 28.6 1.0
OE1 A:GLU152 2.1 24.5 1.0
OE1 A:GLU191 2.2 33.8 1.0
O A:ASN147 2.3 26.4 1.0
O A:HOH402 2.4 27.9 1.0
ZN A:ZN307 3.0 27.4 1.0
CD A:GLU191 3.1 29.8 1.0
C A:ASN147 3.2 26.3 1.0
CD A:GLU152 3.3 25.3 1.0
O A:ACT317 3.3 56.8 1.0
OE2 A:GLU191 3.4 27.9 1.0
CA A:ASN147 3.6 23.4 1.0
OXT A:ACT317 3.6 47.0 1.0
O A:HOH548 3.7 42.8 1.0
CB A:ASN147 3.8 26.6 1.0
OE2 A:GLU152 3.8 27.4 1.0
C A:ACT317 3.9 56.1 1.0
N A:ASP148 4.4 22.6 1.0
CG A:GLU152 4.5 22.4 1.0
CG A:GLU191 4.5 29.8 1.0
CB A:GLU152 4.6 18.8 1.0
CA A:ASP148 4.8 23.0 1.0
CG A:ASN147 4.8 27.1 1.0
C A:ASP148 4.8 20.7 1.0
CB A:GLU191 5.0 29.6 1.0
N A:ASN147 5.0 23.1 1.0
N A:ALA149 5.0 22.6 1.0

Zinc binding site 6 out of 11 in 6jf1

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Zinc binding site 6 out of 11 in the Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:27.4
occ:1.00
 O A:HOH402 1.9 27.9 1.0
OE2 A:GLU191 2.0 27.9 1.0
OE2 A:GLU152 2.1 27.4 1.0
CD A:GLU152 2.7 25.3 1.0
OE1 A:GLU152 2.7 24.5 1.0
CD A:GLU191 3.0 29.8 1.0
ZN A:ZN306 3.0 38.6 1.0
OXT A:ACT317 3.3 47.0 1.0
OE1 A:GLU191 3.3 33.8 1.0
O A:ACT317 3.6 56.8 1.0
O A:HOH548 3.6 42.8 1.0
O A:HOH413 3.6 28.6 1.0
C A:ACT317 3.8 56.1 1.0
CG A:GLU152 4.2 22.4 1.0
CB A:THR176 4.3 32.0 1.0
N A:VAL177 4.3 26.5 1.0
CG2 A:VAL177 4.3 25.7 1.0
CG A:GLU191 4.3 29.8 1.0
CA A:THR176 4.7 28.9 1.0
CB A:VAL177 4.7 26.7 1.0
CG2 A:THR176 4.9 30.9 1.0
CB A:GLU191 4.9 29.6 1.0

Zinc binding site 7 out of 11 in 6jf1

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Zinc binding site 7 out of 11 in the Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:36.6
occ:0.85
 NE2 A:HIS-12 2.1 41.3 1.0
O A:ACT315 2.2 35.3 1.0
NE2 A:HIS-14 2.4 42.7 1.0
OD1 A:ASP52 2.4 33.2 1.0
O A:HOH444 2.5 38.6 1.0
C A:ACT315 2.9 37.1 1.0
ZN A:ZN305 2.9 41.0 0.8
OXT A:ACT315 3.0 40.2 1.0
CE1 A:HIS-12 3.1 39.4 1.0
CD2 A:HIS-14 3.1 38.0 1.0
CD2 A:HIS-12 3.1 40.0 1.0
CE1 A:HIS-14 3.5 33.8 1.0
CG A:ASP52 3.5 31.8 1.0
O A:HOH540 3.8 33.6 1.0
OD2 A:ASP52 3.8 35.5 1.0
CL A:CL313 3.9 64.4 1.0
CH3 A:ACT315 4.1 33.5 1.0
ND1 A:HIS-12 4.2 39.5 1.0
CG A:HIS-12 4.3 43.5 1.0
CG A:HIS-14 4.3 37.0 1.0
ND1 A:HIS-14 4.4 36.0 1.0
CB A:ASP52 4.8 23.4 1.0
CA A:ASP52 4.9 22.0 1.0
N A:ASP52 5.0 19.7 1.0

Zinc binding site 8 out of 11 in 6jf1

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Zinc binding site 8 out of 11 in the Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:39.4
occ:1.00
 ND1 A:HIS-15 2.1 19.8 1.0
NE2 A:HIS-13 2.2 45.5 1.0
OXT A:ACT320 2.3 36.0 1.0
O A:HOH519 2.5 24.9 1.0
CE1 A:HIS-15 3.0 20.3 1.0
C A:ACT320 3.0 35.1 1.0
CG A:HIS-15 3.0 17.6 1.0
CH3 A:ACT320 3.1 19.9 1.0
CD2 A:HIS-13 3.1 42.2 1.0
CE1 A:HIS-13 3.2 41.9 1.0
CB A:HIS-15 3.4 18.3 1.0
O A:PHE67 4.0 18.9 1.0
NE2 A:HIS-15 4.1 19.5 1.0
OG1 A:THR68 4.1 20.0 1.0
CD2 A:HIS-15 4.1 18.1 1.0
O A:ACT320 4.2 39.9 1.0
CG A:HIS-13 4.3 40.5 1.0
ND1 A:HIS-13 4.3 45.0 1.0
CA A:HIS-15 4.5 19.2 1.0
OE1 A:GLU66 4.5 42.1 1.0
C A:PHE67 4.6 22.1 1.0
CB A:GLU66 4.9 24.2 1.0
O A:HOH504 4.9 37.5 1.0
N A:THR68 5.0 20.1 1.0

Zinc binding site 9 out of 11 in 6jf1

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Zinc binding site 9 out of 11 in the Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:42.4
occ:1.00
 O A:HOH532 1.9 37.2 1.0
OE1 A:GLU84 2.2 33.5 1.0
CD A:GLU84 3.1 37.6 1.0
ZN A:ZN312 3.2 59.0 0.8
OE2 A:GLU84 3.4 43.5 1.0
CH3 A:ACT316 4.0 27.3 1.0
O A:HOH570 4.3 42.2 1.0
CG A:GLU84 4.5 34.9 1.0
CB A:GLU84 4.8 30.0 1.0

Zinc binding site 10 out of 11 in 6jf1

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Zinc binding site 10 out of 11 in the Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Substrate Binding Protein of A Methionine Transporter From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn311

b:50.6
occ:0.80
 OD2 A:ASP220 1.9 43.9 1.0
O A:ACT321 2.5 65.2 1.0
CG A:ASP220 2.7 32.7 1.0
OD1 A:ASP220 2.9 32.5 1.0
C A:ACT321 3.0 67.1 1.0
CE A:LYS222 3.3 53.3 1.0
O A:HOH442 3.5 58.8 1.0
CH3 A:ACT321 3.6 65.7 1.0
OXT A:ACT321 3.7 67.3 1.0
NZ A:LYS222 4.1 61.6 1.0
CB A:ASP220 4.2 32.2 1.0
CB A:LYS222 4.2 36.5 1.0
O A:HOH428 4.2 64.8 1.0
CD A:LYS222 4.4 49.7 1.0
NZ A:LYS223 4.5 45.1 1.0
CE A:LYS223 4.7 43.3 1.0
CG A:LYS222 4.8 37.9 1.0

Reference:

B.Jha, R.Vyas, J.Bhushan, D.Sehgal, B.K.Biswal. Crystal Structure of A Methionine Transporter Protein To Be Published.
Page generated: Wed Dec 16 12:04:25 2020

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