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Zinc in PDB 4rs3: Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol

Enzymatic activity of Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol

All present enzymatic activity of Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol:
3.6.3.17;

Protein crystallography data

The structure of Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol, PDB code: 4rs3 was solved by Y.Patskovsky, R.Toro, R.Bhosle, N.Al Obaidi, L.L.Morisco, S.R.Wasserman, S.Chamala, J.D.Attonito, A.Scott Glenn, S.Chowdhury, J.Lafleur, R.D.Hillerich, B.Siede, J.Love, K.L.Whalen, J.A.Gerlt, S.C.Almo, Enzymefunction Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.76 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.841, 63.070, 73.134, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 16.3

Other elements in 4rs3:

The structure of Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol also contains other interesting chemical elements:

Chlorine (Cl) 17 atoms

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 Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol (pdb code 4rs3). 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 Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol, PDB code: 4rs3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 4rs3

Go back to Zinc Binding Sites List in 4rs3
Zinc binding site 1 out of 11 in the Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:12.4
occ:1.00
 OD2 A:ASP150 1.9 11.9 1.0
N1 A:IMD413 2.1 11.0 1.0
CL A:CL419 2.2 15.6 1.0
CG A:ASP150 2.8 10.6 1.0
C5 A:IMD413 3.0 11.6 1.0
OD1 A:ASP150 3.1 11.4 1.0
C2 A:IMD413 3.1 13.2 1.0
O A:HOH507 3.8 24.2 1.0
CB A:ASP150 4.2 11.7 1.0
C4 A:IMD413 4.2 12.5 1.0
N3 A:IMD413 4.2 15.3 1.0
C5 A:IMD415 4.6 12.8 0.5
CG A:GLN146 4.6 10.3 1.0
N1 A:IMD415 4.7 18.4 0.5
NE2 A:GLN146 4.9 10.6 1.0

Zinc binding site 2 out of 11 in 4rs3

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Zinc binding site 2 out of 11 in the Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:17.8
occ:0.55
 OE2 A:GLU53 1.9 38.8 1.0
N1 A:IMD414 2.0 23.2 0.6
CL A:CL423 2.2 16.1 0.5
CL A:CL428 2.3 22.7 0.6
CL A:CL423 2.3 19.2 0.5
CD A:GLU53 2.7 19.2 1.0
OE1 A:GLU53 2.9 22.5 1.0
C5 A:IMD414 2.9 18.9 0.6
C2 A:IMD414 3.1 21.9 0.6
C4 A:IMD414 4.1 18.5 0.6
CG A:GLU53 4.1 20.2 1.0
NE A:ARG318 4.2 17.6 1.0
N3 A:IMD414 4.2 22.9 0.6
CD A:ARG318 4.6 22.0 1.0
NE2 A:GLN319 5.0 46.8 1.0

Zinc binding site 3 out of 11 in 4rs3

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Zinc binding site 3 out of 11 in the Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol


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 Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:12.9
occ:1.00
 OD2 A:ASP56 1.9 12.7 1.0
CL A:CL420 2.2 18.5 1.0
CL A:CL421 2.3 15.5 1.0
CG A:ASP56 2.9 11.8 1.0
CB A:ASP56 3.2 12.3 1.0
NZ A:LYS52 3.8 21.8 1.0
O A:HOH699 4.0 33.0 1.0
OD1 A:ASP56 4.1 12.8 1.0
O A:HOH620 4.1 14.0 1.0
O A:HOH580 4.5 46.2 1.0
OXT A:ACT435 4.6 33.2 1.0
O A:HOH698 4.6 24.1 1.0
CE A:LYS52 4.7 17.4 1.0
CA A:ASP56 4.8 11.8 1.0
CG A:LYS52 4.8 11.6 1.0
NZ A:LYS60 4.9 43.2 1.0
O A:LYS52 4.9 10.2 1.0

Zinc binding site 4 out of 11 in 4rs3

Go back to Zinc Binding Sites List in 4rs3
Zinc binding site 4 out of 11 in the Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol


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 Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:16.4
occ:1.00
 OE2 A:GLU252 2.0 20.5 1.0
OE2 A:GLU50 2.0 15.0 1.0
CL A:CL418 2.2 18.9 1.0
CL A:CL417 2.3 16.0 1.0
CD A:GLU50 3.0 17.9 1.0
CD A:GLU252 3.1 21.9 1.0
CG A:GLU50 3.3 12.8 1.0
CG A:GLU252 3.5 18.0 1.0
CB A:GLU252 3.7 11.6 1.0
N A:GLU252 4.0 11.4 1.0
OE1 A:GLU50 4.1 24.0 1.0
OE1 A:GLU252 4.3 25.1 1.0
N3 A:IMD414 4.4 22.9 0.6
CB A:ILE251 4.5 9.5 1.0
CA A:GLU252 4.5 11.2 1.0
CB A:SER46 4.6 10.8 1.0
O A:SER46 4.7 9.6 1.0
CB A:GLU50 4.8 12.4 1.0
C4 A:IMD414 4.8 18.5 0.6
OG A:SER46 5.0 13.3 1.0
C A:ILE251 5.0 9.0 1.0

Zinc binding site 5 out of 11 in 4rs3

Go back to Zinc Binding Sites List in 4rs3
Zinc binding site 5 out of 11 in the Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol


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 Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:30.3
occ:1.00
 O A:HOH711 2.0 28.0 1.0
O A:ACT434 2.1 22.4 1.0
OE2 A:GLU237 2.2 42.3 1.0
N3 A:IMD416 2.3 33.0 1.0
C4 A:IMD416 2.5 36.8 1.0
OE1 A:GLU237 2.7 92.8 1.0
CD A:GLU237 2.7 40.8 1.0
C A:ACT434 3.1 38.4 1.0
OXT A:ACT434 3.3 51.8 1.0
C2 A:IMD416 3.7 30.8 1.0
C5 A:IMD416 3.9 37.1 1.0
NE2 A:GLN233 4.1 48.5 1.0
CG A:GLU237 4.2 27.0 1.0
NZ A:LYS207 4.3 70.7 1.0
CE A:LYS207 4.4 35.2 1.0
CH3 A:ACT434 4.4 32.4 1.0
N1 A:IMD416 4.4 40.4 1.0

Zinc binding site 6 out of 11 in 4rs3

Go back to Zinc Binding Sites List in 4rs3
Zinc binding site 6 out of 11 in the Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol


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 Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:35.6
occ:1.00
 OD1 A:ASP200 1.9 33.3 1.0
CL A:CL432 2.4 42.4 1.0
CL A:CL429 2.6 49.1 1.0
CL A:CL430 2.8 45.1 1.0
CG A:ASP200 2.9 29.5 1.0
OD2 A:ASP200 3.2 34.4 1.0
CB A:ASP200 4.3 18.8 1.0
CA A:ASP200 4.7 12.0 1.0
CG A:ARG199 4.7 20.4 1.0
CG2 A:VAL203 4.7 13.6 1.0
N A:ASP200 4.9 11.5 1.0

Zinc binding site 7 out of 11 in 4rs3

Go back to Zinc Binding Sites List in 4rs3
Zinc binding site 7 out of 11 in the Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol


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 Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:25.6
occ:0.50
 OD2 A:ASP337 1.8 76.6 1.0
O A:HOH708 2.2 25.2 1.0
CG A:ASP337 2.4 26.6 1.0
OD1 A:ASP337 2.5 28.3 1.0
OG1 A:THR347 3.6 30.8 1.0
CB A:ASP337 3.8 20.1 1.0
CB A:THR347 4.1 25.0 1.0
O A:HOH696 4.3 35.2 1.0
O A:HOH604 4.4 13.9 1.0
N A:THR347 4.4 29.4 1.0
CA A:ASP337 4.8 20.5 1.0
CA A:THR347 4.9 25.1 1.0
O A:HOH518 4.9 11.4 1.0

Zinc binding site 8 out of 11 in 4rs3

Go back to Zinc Binding Sites List in 4rs3
Zinc binding site 8 out of 11 in the Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol


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 Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:15.6
occ:0.50
 O A:HOH665 2.0 11.3 0.5
OD2 A:ASP136 2.1 13.8 1.0
O A:HOH670 2.2 24.6 0.5
O A:HOH717 2.2 18.6 0.5
CG A:ASP136 2.9 10.9 1.0
OD1 A:ASP136 2.9 10.4 1.0
CB A:ALA139 4.3 9.8 1.0
CB A:ASP136 4.3 9.4 1.0
N A:ALA139 4.4 8.5 1.0
CB A:VAL138 4.5 8.8 1.0
CA A:ALA139 4.8 7.5 1.0
CG1 A:VAL138 5.0 9.5 1.0

Zinc binding site 9 out of 11 in 4rs3

Go back to Zinc Binding Sites List in 4rs3
Zinc binding site 9 out of 11 in the Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol


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 Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn410

b:13.0
occ:1.00
 OD1 A:ASP178 2.0 11.5 1.0
OXT A:ACT433 2.0 13.3 1.0
CL A:CL422 2.2 15.5 1.0
CG A:ASP178 2.8 11.2 1.0
C A:ACT433 3.0 14.2 1.0
OD2 A:ASP178 3.0 13.2 1.0
CH3 A:ACT433 3.2 12.4 1.0
NZ A:LYS192 4.0 27.8 1.0
O A:ACT433 4.1 15.3 1.0
CB A:ASP178 4.2 8.3 1.0
CD1 A:LEU181 4.4 12.6 1.0
CD A:LYS192 4.6 22.3 1.0
CA A:ASP178 4.7 8.2 1.0
O A:GLY174 4.9 8.8 1.0
CE A:LYS192 5.0 26.2 1.0

Zinc binding site 10 out of 11 in 4rs3

Go back to Zinc Binding Sites List in 4rs3
Zinc binding site 10 out of 11 in the Crystal Structure of Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol


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 Carbohydrate Transporter A0QYB3 From Mycobacterium Smegmatis Str. MC2 155, Target Efi-510969, in Complex with Xylitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn411

b:16.4
occ:0.60
 OXT A:ACT436 1.8 35.4 1.0
OD2 A:ASP218 2.0 14.6 1.0
CL A:CL425 2.2 21.6 0.6
CL A:CL424 2.3 26.5 0.6
CG A:ASP218 2.8 13.8 1.0
C A:ACT436 2.8 29.1 1.0
OD1 A:ASP218 2.9 16.1 1.0
O A:ACT436 3.2 28.1 1.0
ND2 A:ASN157 3.9 17.4 1.0
CH3 A:ACT436 4.2 25.7 1.0
CB A:ASP218 4.2 12.0 1.0
CA A:GLY156 4.2 11.1 1.0
O A:HOH538 4.2 27.4 1.0
N A:ASN157 4.3 10.6 1.0
O A:GLN216 4.4 15.8 1.0
CG A:ASN157 4.5 13.8 1.0
C A:GLY156 4.8 9.3 1.0
CE A:LYS155 4.9 41.5 1.0
CB A:ASN157 5.0 13.2 1.0
CD A:LYS155 5.0 60.0 1.0

Reference:

Y.Patskovsky, R.Toro, R.Bhosle, N.Al Obaidi, S.Chamala, A.Scott Glenn, J.D.Attonito, S.Chowdhury, J.Lafleur, R.D.Siedel, L.L.Morisco, S.R.Wasserman, B.Hillerich, J.Love, K.L.Whalen, J.A.Gerlt, S.C.Almo. Crystal Structure of Carbohydrate Transporter MSMEG_3598 From Mycobacterium Smegmatis, Target Efi-510969 To Be Published.
Page generated: Sun Oct 27 07:21:52 2024

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