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Zinc in PDB 6hbd: Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose

Protein crystallography data

The structure of Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose, PDB code: 6hbd was solved by M.Li, C.Mueller, O.Einsle, C.Jessen-Trefzer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 105.31 / 2.44
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 118.300, 118.300, 231.120, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 26.6

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose (pdb code 6hbd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose, PDB code: 6hbd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in 6hbd

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Zinc binding site 1 out of 15 in the Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose


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 MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:48.5
occ:1.00
O A:HOH506 2.2 8.2 0.5
ND1 A:HIS244 2.3 52.0 1.0
HB3 A:HIS244 2.8 47.9 1.0
CG A:HIS244 3.1 50.5 1.0
HB2 A:HIS244 3.1 47.9 1.0
CB A:HIS244 3.2 47.9 1.0
CE1 A:HIS244 3.4 51.7 1.0
HE1 A:HIS244 3.7 51.6 1.0
CD2 A:HIS244 4.3 52.2 1.0
OD1 A:ASP245 4.4 67.3 1.0
NE2 A:HIS244 4.4 52.3 1.0
O A:HOH514 4.5 50.7 1.0
CA A:HIS244 4.7 47.4 1.0
H A:HIS244 4.9 48.6 1.0
H A:ASP245 4.9 44.0 1.0

Zinc binding site 2 out of 15 in 6hbd

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Zinc binding site 2 out of 15 in the Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose


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 MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:45.0
occ:1.00
OE1 A:GLU291 2.1 48.5 1.0
O A:HOH515 2.1 16.6 1.0
NE2 B:HIS315 2.2 53.3 1.0
OE2 A:GLU260 2.2 56.1 1.0
OE1 A:GLU260 2.4 77.4 1.0
HG2 A:GLU291 2.6 52.3 1.0
CD A:GLU260 2.6 64.0 1.0
CD A:GLU291 3.0 58.3 1.0
CE1 B:HIS315 3.0 53.0 1.0
HE1 B:HIS315 3.2 53.2 1.0
CD2 B:HIS315 3.3 53.0 1.0
CG A:GLU291 3.3 52.8 1.0
HB2 A:ALA312 3.4 42.8 1.0
HZ A:PHE293 3.5 43.6 1.0
HD2 B:HIS315 3.6 53.8 1.0
HH21 A:ARG305 3.6 37.5 1.0
HD23 A:LEU309 3.7 42.0 1.0
HG3 A:GLU291 3.9 52.3 1.0
HB1 A:ALA312 4.1 42.8 1.0
CB A:ALA312 4.1 43.0 1.0
CG A:GLU260 4.1 38.4 1.0
HH22 A:ARG305 4.2 37.5 1.0
OE2 A:GLU291 4.2 53.4 1.0
NH2 A:ARG305 4.2 39.7 1.0
ND1 B:HIS315 4.2 52.7 1.0
HB3 A:ALA312 4.2 42.8 1.0
HA A:LEU309 4.3 37.0 1.0
HB3 A:GLU291 4.3 46.5 1.0
CG B:HIS315 4.3 50.6 1.0
CB A:GLU291 4.5 47.4 1.0
HD21 A:LEU309 4.5 42.0 1.0
CZ A:PHE293 4.5 43.4 1.0
CD2 A:LEU309 4.6 41.1 1.0
HG3 A:GLU260 4.6 39.0 1.0
HB2 A:GLU260 4.6 40.5 1.0
HG2 A:GLU260 4.6 39.0 1.0
HB3 A:GLU260 4.7 40.5 1.0
HE1 A:PHE293 4.8 45.6 1.0
CB A:GLU260 4.8 40.7 1.0
HD22 A:ASN262 4.8 35.1 1.0
HG A:LEU309 4.9 39.7 1.0
O A:LYS308 5.0 41.7 1.0
HB3 A:LYS308 5.0 39.7 1.0

Zinc binding site 3 out of 15 in 6hbd

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Zinc binding site 3 out of 15 in the Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose


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 MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:93.3
occ:1.00
OD1 A:ASP88 1.9 89.5 1.0
OD2 A:ASP112 2.1 0.3 1.0
CG A:ASP88 2.9 89.6 1.0
O A:HOH519 3.2 50.2 1.0
CG A:ASP112 3.2 0.4 1.0
OD2 A:ASP88 3.2 98.0 1.0
HG3 A:GLN92 3.3 69.7 1.0
OD1 A:ASP112 3.8 0.8 1.0
HG2 A:GLN92 4.2 69.7 1.0
CB A:ASP88 4.2 74.8 1.0
CG A:GLN92 4.2 69.7 1.0
HB2 A:ASP112 4.3 84.7 1.0
CB A:ASP112 4.4 85.1 1.0
HB2 A:GLN111 4.4 78.6 1.0
HA A:ASP88 4.4 72.8 1.0
HB2 A:ASP88 4.4 74.7 1.0
O A:ASP88 4.6 76.9 1.0
O A:HOH505 4.6 46.5 1.0
HE21 A:GLN92 4.7 60.5 1.0
CA A:ASP88 4.8 73.0 1.0
CD A:GLN92 4.8 77.4 1.0
C A:ASP88 4.8 76.5 1.0
HB3 A:ASP88 5.0 74.7 1.0
NE2 A:GLN92 5.0 59.3 1.0

Zinc binding site 4 out of 15 in 6hbd

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Zinc binding site 4 out of 15 in the Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose


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 MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:87.7
occ:1.00
OD1 A:ASP158 2.2 65.3 1.0
OD2 A:ASP162 2.2 68.4 1.0
CG A:ASP158 3.1 61.9 1.0
CG A:ASP162 3.1 65.2 1.0
HH21 A:ARG84 3.3 64.1 1.0
OD2 A:ASP158 3.4 58.0 1.0
OD1 A:ASP162 3.4 65.8 1.0
HE A:ARG84 3.4 67.8 1.0
HD2 A:PHE124 3.6 48.9 1.0
HB3 A:ALA107 4.0 59.0 1.0
NH2 A:ARG84 4.2 63.0 1.0
HD11 A:ILE125 4.3 49.5 1.0
NE A:ARG84 4.3 68.5 1.0
HD12 A:ILE125 4.4 49.5 1.0
HB2 A:ALA107 4.5 59.0 1.0
CB A:ASP158 4.5 54.3 1.0
CB A:ASP162 4.5 56.7 1.0
CD2 A:PHE124 4.6 49.6 1.0
HB2 A:ASP162 4.7 56.6 1.0
HE2 A:PHE119 4.7 56.8 1.0
HE2 A:PHE124 4.7 51.6 1.0
CB A:ALA107 4.7 59.1 1.0
O A:ASP158 4.7 52.8 1.0
CZ A:ARG84 4.7 84.1 1.0
HA A:ASP158 4.8 52.4 1.0
HB2 A:PHE124 4.8 45.1 1.0
CD1 A:ILE125 4.8 49.9 1.0
HB3 A:ASP162 4.8 56.6 1.0
HB2 A:ASP158 4.9 54.9 1.0
HH22 A:ARG84 5.0 64.1 1.0

Zinc binding site 5 out of 15 in 6hbd

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Zinc binding site 5 out of 15 in the Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose


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 MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:67.8
occ:1.00
NE2 A:HIS318 2.0 63.2 1.0
NE2 A:HIS316 2.2 56.2 1.0
O A:HOH501 2.4 46.5 1.0
CE1 A:HIS318 3.0 62.7 1.0
CD2 A:HIS318 3.0 63.6 1.0
CD2 A:HIS316 3.1 56.5 1.0
CE1 A:HIS316 3.2 55.6 1.0
HE1 A:HIS318 3.2 63.0 1.0
HD2 A:HIS316 3.3 55.6 1.0
HD2 A:HIS318 3.3 63.6 1.0
HH21 B:ARG130 3.4 84.9 1.0
HH22 B:ARG130 3.4 84.9 1.0
HE1 A:HIS316 3.4 54.9 1.0
NH2 B:ARG130 3.7 85.6 1.0
ND1 A:HIS318 4.1 63.1 1.0
CG A:HIS318 4.2 61.6 1.0
CG A:HIS316 4.3 53.4 1.0
OE2 A:GLU268 4.3 99.5 1.0
ND1 A:HIS316 4.3 55.5 1.0
HG13 A:VAL286 4.4 67.5 1.0
HG22 A:VAL286 4.7 67.7 1.0
HD3 B:ARG130 4.7 82.2 1.0
CD A:GLU268 4.8 95.6 1.0
HG11 A:VAL286 4.8 67.5 1.0
CZ B:ARG130 4.8 94.2 1.0
HG2 A:PRO283 4.9 72.9 1.0
HG3 A:PRO283 4.9 72.9 1.0
OE1 A:GLU268 5.0 91.2 1.0

Zinc binding site 6 out of 15 in 6hbd

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Zinc binding site 6 out of 15 in the Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose


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 MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:69.9
occ:1.00
OE1 B:GLU126 1.9 31.0 1.0
ND1 A:HIS318 2.1 63.1 1.0
O B:HOH511 2.2 47.0 1.0
NE2 A:HIS320 2.4 67.8 1.0
HE1 A:HIS318 2.7 63.0 1.0
CE1 A:HIS318 2.7 62.7 1.0
CD B:GLU126 3.0 56.6 1.0
CE1 A:HIS320 3.3 67.5 1.0
HD3 B:ARG130 3.3 82.2 1.0
CG A:HIS318 3.4 61.6 1.0
HE1 A:HIS320 3.4 67.3 1.0
HB2 A:HIS318 3.4 58.3 1.0
HG2 B:ARG130 3.4 77.0 1.0
CD2 A:HIS320 3.5 68.2 1.0
OE2 B:GLU126 3.5 61.9 1.0
HG2 B:ARG129 3.7 70.9 1.0
HD2 A:HIS320 3.8 67.9 1.0
CB A:HIS318 4.0 58.4 1.0
NE2 A:HIS318 4.0 63.2 1.0
HG3 A:PRO283 4.0 72.9 1.0
CD B:ARG130 4.1 81.8 1.0
CG B:GLU126 4.1 59.7 1.0
HG3 B:GLU126 4.1 59.9 1.0
HD2 B:ARG130 4.2 82.2 1.0
CG B:ARG130 4.2 76.9 1.0
CD2 A:HIS318 4.3 63.6 1.0
HG2 B:GLU126 4.4 59.9 1.0
ND1 A:HIS320 4.5 68.6 1.0
HB3 A:HIS318 4.5 58.3 1.0
HD3 B:ARG129 4.6 77.7 1.0
CG A:HIS320 4.6 67.7 1.0
HB3 B:ARG129 4.6 61.7 1.0
CG B:ARG129 4.7 70.5 1.0
HA B:ARG130 4.7 67.4 1.0
HB3 A:PRO283 4.7 69.1 1.0
HG3 B:ARG130 4.8 77.0 1.0
H A:HIS318 4.8 58.9 1.0
HH21 B:ARG130 4.8 84.9 1.0
HE B:ARG129 4.9 91.0 1.0

Zinc binding site 7 out of 15 in 6hbd

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Zinc binding site 7 out of 15 in the Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose


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 MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:60.0
occ:1.00
NE2 A:HIS319 1.9 68.5 1.0
NE2 A:HIS317 1.9 67.4 1.0
O A:HOH518 2.2 26.9 1.0
CE1 A:HIS319 2.6 68.1 1.0
HE1 A:HIS319 2.7 68.1 1.0
CE1 A:HIS317 2.8 67.0 1.0
CD2 A:HIS317 3.0 67.4 1.0
HE1 A:HIS317 3.0 66.8 1.0
ZN B:ZN403 3.0 57.9 1.0
HG11 A:VAL287 3.1 58.7 1.0
CD2 A:HIS319 3.1 69.1 1.0
HD2 A:HIS317 3.3 67.2 1.0
NE2 B:HIS317 3.5 65.6 1.0
HD2 A:HIS319 3.6 68.9 1.0
ND1 A:HIS319 3.8 68.8 1.0
O B:HOH508 3.9 30.8 1.0
CG1 A:VAL287 4.0 58.8 1.0
ND1 A:HIS317 4.0 67.1 1.0
HG13 A:VAL287 4.0 58.7 1.0
CG A:HIS319 4.0 67.1 1.0
CD2 B:HIS317 4.1 66.0 1.0
CG A:HIS317 4.1 64.6 1.0
HD2 B:HIS317 4.1 66.2 1.0
HG21 A:VAL287 4.2 58.7 1.0
CE1 B:HIS317 4.2 65.1 1.0
HE1 B:HIS317 4.5 65.5 1.0
HG12 A:VAL287 4.5 58.7 1.0
HE1 B:HIS319 4.6 66.5 1.0
HD1 A:HIS319 4.7 68.5 1.0
NE2 B:HIS319 4.8 66.8 1.0
HG22 A:VAL287 4.8 58.7 1.0
CE1 B:HIS319 4.8 66.5 1.0
CG2 A:VAL287 4.9 58.8 1.0
HD1 A:HIS317 4.9 67.1 1.0

Zinc binding site 8 out of 15 in 6hbd

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Zinc binding site 8 out of 15 in the Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose


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 MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:0.7
occ:1.00
OE2 A:GLU37 1.9 0.1 1.0
CD A:GLU37 3.0 0.9 1.0
HG2 A:GLU37 3.4 72.2 1.0
HB3 A:SER41 3.7 63.5 1.0
CG A:GLU37 3.8 72.7 1.0
OE1 A:GLU37 3.9 98.7 1.0
HG3 A:GLU37 4.2 72.2 1.0
CB A:SER41 4.7 63.6 1.0
HA A:GLU37 4.8 56.0 1.0
HA A:SER41 4.8 59.9 1.0
H A:SER41 5.0 59.8 1.0

Zinc binding site 9 out of 15 in 6hbd

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Zinc binding site 9 out of 15 in the Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose


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 MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:0.1
occ:1.00
OE2 A:GLU284 3.7 0.8 1.0
OD1 A:ASP114 4.2 0.5 1.0
CD A:GLU284 4.8 0.9 1.0

Zinc binding site 10 out of 15 in 6hbd

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Zinc binding site 10 out of 15 in the Crystal Structure of MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose


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 MSMEG_1712 From Mycobacterium Smegmatis in Complex with Beta-D-Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:0.8
occ:1.00
OD2 B:ASP162 2.6 97.4 1.0
OD1 B:ASP158 2.8 95.3 1.0
CG B:ASP162 3.5 91.7 1.0
OD1 B:ASP162 3.6 93.4 1.0
CG B:ASP158 3.7 91.5 1.0
OD2 B:ASP158 3.9 92.6 1.0
HD11 B:ILE125 4.1 68.6 1.0
HB3 B:ALA107 4.1 90.2 1.0
HD2 B:PHE124 4.2 60.0 1.0
HD12 B:ILE125 4.4 68.6 1.0
HH22 B:ARG84 4.6 0.1 1.0
HB2 B:ALA107 4.6 90.2 1.0
NH2 B:ARG84 4.7 0.3 1.0
CD1 B:ILE125 4.7 66.9 1.0
HE2 B:PHE119 4.8 61.6 1.0
HH12 B:ARG84 4.8 0.2 1.0
CB B:ALA107 4.8 90.6 1.0
CB B:ASP162 4.9 77.4 1.0
CZ B:ARG84 4.9 0.7 1.0
NH1 B:ARG84 4.9 0.1 1.0

Reference:

M.Li, C.Muller, K.Frohlich, O.Gorka, L.Zhang, O.Gross, O.Schilling, O.Einsle, C.Jessen-Trefzer. Detection and Characterization of A Mycobacterial L-Arabinofuranose Abc Transporter Identified with A Rapid Lipoproteomics Protocol. Cell Chem Biol V. 26 852 2019.
ISSN: ESSN 2451-9456
PubMed: 31006617
DOI: 10.1016/J.CHEMBIOL.2019.03.002
Page generated: Wed Dec 16 11:56:22 2020

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