Zinc in PDB 4bf7: Emericilla Nidulans Endo-Beta-1,4-Galactanase

All present enzymatic activity of Emericilla Nidulans Endo-Beta-1,4-Galactanase:
3.2.1.89;

The structure of Emericilla Nidulans Endo-Beta-1,4-Galactanase, PDB code: 4bf7 was solved by H.Otten, M.Michalak, S.Larsen, J.D.Mikkelsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.475 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.900, 72.370, 98.380, 90.00, 90.00, 90.00
R / Rfree (%)	15.75 / 19.23

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Emericilla Nidulans Endo-Beta-1,4-Galactanase (pdb code 4bf7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the Emericilla Nidulans Endo-Beta-1,4-Galactanase, PDB code: 4bf7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in the Emericilla Nidulans Endo-Beta-1,4-Galactanase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Emericilla Nidulans Endo-Beta-1,4-Galactanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:20.1 occ:0.90 OE1 A:GLU275 2.0 25.0 1.0 OD2 A:ASP332 2.0 23.4 1.0 O A:HOH2162 2.0 28.8 1.0 CD A:GLU275 2.8 22.9 1.0 CG A:ASP332 2.9 27.6 1.0 OE2 A:GLU275 2.9 26.6 1.0 HB3 A:ASP332 3.0 30.9 1.0 O A:HOH2163 3.2 12.9 1.0 CB A:ASP332 3.3 25.7 1.0 HB2 A:ASP332 3.3 30.9 1.0 HA A:VAL329 3.9 24.0 1.0 OD1 A:ASP332 3.9 24.0 1.0 O A:HOH2161 3.9 28.2 1.0 HB3 A:GLU275 4.1 22.7 1.0 CG A:GLU275 4.2 23.4 1.0 HG21 A:VAL329 4.5 28.6 1.0 CB A:GLU275 4.6 18.9 1.0 HG2 A:GLU275 4.7 28.1 1.0 HG3 A:GLU275 4.7 28.1 1.0 CA A:ASP332 4.8 27.1 1.0 CA A:VAL329 4.9 20.0 1.0 HB2 A:GLU275 4.9 22.7 1.0 OG A:SER328 4.9 23.9 1.0

Zinc binding site 2 out of 15 in the Emericilla Nidulans Endo-Beta-1,4-Galactanase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Emericilla Nidulans Endo-Beta-1,4-Galactanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:22.4 occ:1.00 O A:ACT1339 1.8 27.4 1.0 OD2 A:ASP320 1.9 19.3 1.0 OD2 A:ASP317 2.0 25.0 1.0 CG A:ASP320 2.7 25.6 1.0 CG A:ASP317 2.9 20.8 1.0 OD1 A:ASP320 2.9 19.7 1.0 HB3 A:ASP317 3.0 20.5 1.0 C A:ACT1339 3.1 29.0 1.0 CB A:ASP317 3.2 17.1 1.0 HB2 A:ASP317 3.3 20.5 1.0 OXT A:ACT1339 3.7 30.5 1.0 H3 A:ACT1339 3.9 35.8 1.0 OD1 A:ASP317 4.0 21.6 1.0 HH21 A:ARG319 4.1 56.9 1.0 CH3 A:ACT1339 4.1 29.8 1.0 O A:HOH2171 4.1 31.9 1.0 CB A:ASP320 4.1 22.0 1.0 HB A:THR322 4.2 29.9 1.0 NH2 A:ARG319 4.3 47.4 1.0 HB3 A:ASP320 4.3 26.4 1.0 HB2 A:ARG319 4.3 32.1 1.0 HH22 A:ARG319 4.3 56.9 1.0 H A:ASP320 4.5 29.7 1.0 HB2 A:ASP320 4.6 26.4 1.0 H1 A:ACT1339 4.7 35.8 1.0 CA A:ASP317 4.8 15.6 1.0 H2 A:ACT1339 4.8 35.8 1.0 N A:ASP320 4.9 24.8 1.0 CZ A:ARG319 4.9 57.1 1.0

Zinc binding site 3 out of 15 in the Emericilla Nidulans Endo-Beta-1,4-Galactanase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Emericilla Nidulans Endo-Beta-1,4-Galactanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:26.1 occ:0.73 O A:HOH2013 1.9 19.6 1.0 OD2 A:ASP302 2.0 41.5 1.0 OE1 A:GLU15 2.0 30.3 1.0 O A:HOH2014 2.1 31.2 1.0 HB2 A:ASP302 2.7 32.0 1.0 CG A:ASP302 2.9 36.7 1.0 CD A:GLU15 3.0 24.8 1.0 CB A:ASP302 3.2 26.7 1.0 HG A:SER18 3.3 41.3 1.0 HG23 A:ILE14 3.3 24.6 1.0 OE2 A:GLU15 3.4 26.2 1.0 HE1 A:TRP300 3.4 20.8 1.0 HB3 A:ASP302 3.4 32.0 1.0 HA A:GLU15 3.9 19.9 1.0 HG22 A:ILE14 4.0 24.6 1.0 CG2 A:ILE14 4.0 20.5 1.0 OG A:SER18 4.0 34.4 1.0 OD1 A:ASP302 4.1 40.5 1.0 NE1 A:TRP300 4.2 17.3 1.0 CG A:GLU15 4.3 18.1 1.0 HG2 A:GLU15 4.3 21.8 1.0 HD1 A:TRP300 4.4 24.9 1.0 H A:ASP302 4.4 25.2 1.0 HB2 A:SER18 4.5 32.7 1.0 HG21 A:ILE14 4.5 24.6 1.0 CA A:ASP302 4.7 24.4 1.0 CD1 A:TRP300 4.7 20.7 1.0 CA A:GLU15 4.7 16.6 1.0 CB A:SER18 4.7 27.3 1.0 N A:GLU15 4.8 15.8 1.0 HB3 A:SER18 4.8 32.7 1.0 O A:ILE14 5.0 16.2 1.0 HG3 A:GLU15 5.0 21.8 1.0 N A:ASP302 5.0 21.0 1.0 C A:ILE14 5.0 20.7 1.0

Zinc binding site 4 out of 15 in the Emericilla Nidulans Endo-Beta-1,4-Galactanase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Emericilla Nidulans Endo-Beta-1,4-Galactanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:41.1 occ:0.66 HD1 A:HIS150 1.8 42.2 1.0 O A:HOH2094 2.2 41.0 1.0 OD1 A:ASP152 2.5 31.1 1.0 ND1 A:HIS150 2.6 35.2 1.0 OD2 A:ASP152 2.6 34.3 1.0 HB3 A:HIS150 2.9 26.0 1.0 CG A:ASP152 2.9 32.5 1.0 HA A:HIS150 3.2 27.0 1.0 CG A:HIS150 3.4 31.3 1.0 CB A:HIS150 3.5 21.7 1.0 CE1 A:HIS150 3.7 34.0 1.0 CA A:HIS150 3.8 22.5 1.0 HE1 A:HIS150 3.9 40.8 1.0 H A:ASN153 4.3 25.1 1.0 OD1 A:ASN153 4.3 19.7 1.0 HB2 A:HIS150 4.4 26.0 1.0 O A:ASP149 4.5 22.0 1.0 CB A:ASP152 4.5 21.6 1.0 H A:ASP152 4.5 18.3 1.0 HD22 A:ASN153 4.6 27.8 1.0 CG A:ASN153 4.6 22.4 1.0 CD2 A:HIS150 4.6 30.8 1.0 ND2 A:ASN153 4.7 23.2 1.0 C A:HIS150 4.7 20.4 1.0 NE2 A:HIS150 4.7 34.0 1.0 HB3 A:ASP152 4.8 25.9 1.0 HB2 A:ASP152 4.9 25.9 1.0 N A:HIS150 4.9 22.0 1.0 N A:ASN153 5.0 20.9 1.0

Zinc binding site 5 out of 15 in the Emericilla Nidulans Endo-Beta-1,4-Galactanase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Emericilla Nidulans Endo-Beta-1,4-Galactanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:23.4 occ:0.41 HZ3 A:LYS166 1.2 23.4 1.0 HZ1 A:LYS166 1.7 23.4 1.0 NZ A:LYS166 1.8 19.5 1.0 O A:HOH2100 2.0 41.3 1.0 O A:HOH2099 2.2 33.1 1.0 HZ2 A:LYS166 2.2 23.4 1.0 HD3 A:LYS166 2.9 22.4 1.0 CE A:LYS166 3.0 19.0 1.0 O A:HOH2104 3.1 31.4 1.0 CD A:LYS166 3.4 18.6 1.0 HG2 A:LYS166 3.4 24.3 1.0 HE3 A:LYS166 3.4 22.8 1.0 O A:THR205 3.5 19.9 1.0 HE2 A:LYS166 3.7 22.8 1.0 HD13 A:ILE176 3.8 34.1 1.0 CG A:LYS166 3.9 20.3 1.0 HA A:ASP206 4.2 20.7 1.0 HD2 A:LYS166 4.2 22.4 1.0 HG3 A:LYS166 4.3 24.3 1.0 O A:HOH2126 4.5 16.5 1.0 O A:ASP206 4.6 20.8 1.0 OD1 A:ASP208 4.6 28.9 1.0 C A:THR205 4.6 20.0 1.0 HB A:THR205 4.7 25.1 1.0 CD1 A:ILE176 4.7 28.4 1.0 OD2 A:ASP208 4.8 19.4 1.0 HD12 A:ILE176 4.8 34.1 1.0 C A:ASP206 4.9 19.5 1.0 CA A:ASP206 4.9 17.3 1.0

Zinc binding site 6 out of 15 in the Emericilla Nidulans Endo-Beta-1,4-Galactanase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Emericilla Nidulans Endo-Beta-1,4-Galactanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:40.7 occ:0.64 O A:ACT1346 1.7 21.6 1.0 O A:ACT1345 1.9 29.5 1.0 OD1 A:ASP287 2.4 28.5 1.0 OD1 A:ASP283 2.4 37.5 1.0 OD2 A:ASP287 2.8 39.0 1.0 OD2 A:ASP283 2.8 32.6 1.0 C A:ACT1346 2.9 38.4 1.0 CG A:ASP287 2.9 30.9 1.0 CG A:ASP283 2.9 31.2 1.0 C A:ACT1345 3.0 41.2 1.0 OXT A:ACT1345 3.5 50.3 1.0 OXT A:ACT1346 3.5 52.0 1.0 H3 A:ACT1346 3.9 52.2 1.0 CH3 A:ACT1346 4.0 43.5 1.0 H3 A:ACT1345 4.1 48.9 1.0 CH3 A:ACT1345 4.1 40.7 1.0 O A:ASP283 4.3 25.8 1.0 CB A:ASP283 4.4 25.7 1.0 CB A:ASP287 4.4 28.5 1.0 H2 A:ACT1345 4.6 48.9 1.0 H2 A:ACT1346 4.7 52.2 1.0 H1 A:ACT1346 4.7 52.2 1.0 C A:ASP283 4.7 23.4 1.0 HB2 A:ASP283 4.8 30.8 1.0 HA A:ASP287 4.8 37.7 1.0 HB2 A:ASP287 4.8 34.2 1.0 HZ2 A:LYS228 4.9 59.0 1.0 HB3 A:ASP287 4.9 34.2 1.0 HA A:ASP283 4.9 25.2 1.0 HB3 A:ASP283 4.9 30.8 1.0 CA A:ASP283 5.0 21.0 1.0 H1 A:ACT1345 5.0 48.9 1.0

Zinc binding site 7 out of 15 in the Emericilla Nidulans Endo-Beta-1,4-Galactanase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Emericilla Nidulans Endo-Beta-1,4-Galactanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:22.8 occ:0.75 O3 A:GOL1343 1.9 36.0 1.0 OE2 A:GLU136 2.0 28.4 1.0 OE1 A:GLU246 2.0 18.9 1.0 O A:ACT1336 2.1 29.9 1.0 O1 A:GOL1343 2.1 40.6 1.0 O2 A:GOL1343 2.5 40.3 1.0 CD A:GLU136 2.8 25.9 1.0 CD A:GLU246 2.9 26.9 1.0 C3 A:GOL1343 2.9 35.0 1.0 OE1 A:GLU136 3.0 22.9 1.0 C2 A:GOL1343 3.0 39.1 1.0 OE2 A:GLU246 3.0 24.4 1.0 HO2 A:GOL1343 3.1 48.4 1.0 C1 A:GOL1343 3.1 36.7 1.0 C A:ACT1336 3.1 30.2 1.0 H11 A:GOL1343 3.4 42.0 1.0 OXT A:ACT1336 3.4 24.6 1.0 HG A:SER213 3.4 21.9 1.0 HE2 A:TYR215 3.5 23.2 1.0 HH A:TYR215 3.6 21.3 1.0 H31 A:GOL1343 3.8 44.0 1.0 HD22 A:ASN135 3.8 16.2 1.0 H12 A:GOL1343 3.8 42.0 1.0 H32 A:GOL1343 3.9 44.0 1.0 H2 A:GOL1343 4.1 46.9 1.0 OG A:SER213 4.1 18.3 1.0 OH A:TYR215 4.2 17.8 1.0 CG A:GLU136 4.2 18.4 1.0 O A:HOH2180 4.2 36.4 1.0 CE2 A:TYR215 4.3 19.3 1.0 CG A:GLU246 4.3 23.9 1.0 HG3 A:GLU136 4.3 22.0 1.0 HE1 A:HIS179 4.4 19.6 1.0 HB3 A:SER213 4.5 22.4 1.0 CH3 A:ACT1336 4.5 30.1 1.0 HG2 A:GLU136 4.5 22.0 1.0 HB3 A:GLU246 4.5 18.9 1.0 H3 A:ACT1336 4.6 36.1 1.0 ND2 A:ASN135 4.6 13.5 1.0 HB2 A:GLU246 4.7 18.9 1.0 CZ A:TYR215 4.7 16.2 1.0 HG2 A:GLU246 4.7 28.7 1.0 CB A:GLU246 4.8 15.8 1.0 CB A:SER213 4.8 18.6 1.0 HG3 A:GLU246 4.9 28.7 1.0 HD21 A:ASN135 4.9 16.2 1.0 HE2 A:HIS179 5.0 20.3 1.0

Zinc binding site 8 out of 15 in the Emericilla Nidulans Endo-Beta-1,4-Galactanase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Emericilla Nidulans Endo-Beta-1,4-Galactanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:27.4 occ:0.83 ND1 A:HIS143 2.1 27.4 1.0 O A:HOH2175 2.2 29.2 1.0 O A:HOH2174 2.4 27.4 1.0 HB3 A:HIS143 2.9 22.4 1.0 CE1 A:HIS143 3.1 20.7 1.0 CG A:HIS143 3.1 21.4 1.0 HE1 A:HIS143 3.2 24.9 1.0 CB A:HIS143 3.5 18.7 1.0 HB2 A:HIS143 3.8 22.4 1.0 HB2 A:SER147 4.0 24.9 1.0 HB3 A:SER147 4.1 24.9 1.0 HA A:PRO144 4.2 22.4 1.0 NE2 A:HIS143 4.2 19.9 1.0 CD2 A:HIS143 4.3 21.0 1.0 CB A:SER147 4.5 20.8 1.0 CA A:HIS143 4.9 17.4 1.0 HA A:HIS143 4.9 20.9 1.0 HE2 A:HIS143 5.0 23.8 1.0 O A:HOH2090 5.0 23.6 1.0

Zinc binding site 9 out of 15 in the Emericilla Nidulans Endo-Beta-1,4-Galactanase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Emericilla Nidulans Endo-Beta-1,4-Galactanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn409 b:21.3 occ:1.00 HN3 A:IMD1342 1.2 32.9 1.0 O A:HOH2097 2.0 20.9 1.0 N1 A:IMD1342 2.1 27.4 1.0 NE2 A:HIS159 2.1 18.0 1.0 C2 A:IMD1342 2.9 22.8 1.0 H2 A:IMD1342 3.0 27.3 1.0 CD2 A:HIS159 3.0 16.8 1.0 CE1 A:HIS159 3.1 17.0 1.0 HD2 A:HIS159 3.2 20.2 1.0 C5 A:IMD1342 3.2 26.6 1.0 HE1 A:HIS159 3.3 20.4 1.0 H4 A:IMD1342 3.5 32.0 1.0 N3 A:IMD1342 4.1 29.0 1.0 CG A:HIS159 4.2 16.6 1.0 ND1 A:HIS159 4.2 17.7 1.0 C4 A:IMD1342 4.3 27.4 1.0 HD1 A:HIS159 5.0 21.2 1.0 HN1 A:IMD1342 5.0 34.8 1.0

Zinc binding site 10 out of 15 in the Emericilla Nidulans Endo-Beta-1,4-Galactanase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Emericilla Nidulans Endo-Beta-1,4-Galactanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn410 b:16.6 occ:1.00 OXT A:ACT1337 1.8 24.6 1.0 O A:ACT1344 1.8 24.8 1.0 OD2 A:ASP17 1.9 19.3 1.0 OD1 A:ASP17 2.5 23.9 1.0 CG A:ASP17 2.5 21.0 1.0 C A:ACT1344 3.0 32.8 1.0 C A:ACT1337 3.0 27.9 1.0 OXT A:ACT1344 3.6 25.4 1.0 O A:ACT1337 3.7 27.1 1.0 H3 A:ACT1344 3.9 31.5 1.0 CB A:ASP17 4.0 18.2 1.0 CH3 A:ACT1337 4.1 15.9 1.0 CH3 A:ACT1344 4.1 26.2 1.0 H2 A:ACT1337 4.2 19.1 1.0 H1 A:ACT1337 4.2 19.1 1.0 HB3 A:LEU13 4.3 18.6 1.0 HB2 A:ASP17 4.3 21.8 1.0 O A:LEU13 4.4 14.8 1.0 HB3 A:ASP17 4.4 21.8 1.0 HG A:LEU13 4.6 32.4 1.0 H1 A:ACT1344 4.7 31.5 1.0 H2 A:ACT1344 4.8 31.5 1.0 HA A:ASP17 4.9 25.8 1.0 O A:HOH2016 4.9 32.0 1.0 H3 A:ACT1337 5.0 19.1 1.0

H.Otten, M.Michalak, J.D.Mikkelsen, S.Larsen. The Binding of Zinc Ions to Emericella Nidulans Endo-[Beta]-1,4-Galactanase Is Essential For Crystal Formation Acta Crystallogr.,Sect.F V. 69 850 2013.
ISSN: ISSN 1744-3091
PubMed: 23908026
DOI: 10.1107/S1744309113019714